From cdefaae0fb3256a535d3f300af9dcbf5c9a2ce13 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Tue, 6 Oct 2020 22:05:05 +0200
Subject: [PATCH 01/20] Fix duplicates in intersectin of multiindexes

---
 doc/source/whatsnew/v1.1.4.rst            |  3 ++-
 pandas/core/indexes/multi.py              |  6 ++++--
 pandas/tests/indexes/multi/test_setops.py | 14 ++++++++++++++
 3 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/doc/source/whatsnew/v1.1.4.rst b/doc/source/whatsnew/v1.1.4.rst
index e63912ebc8fee..9d3e503f518f4 100644
--- a/doc/source/whatsnew/v1.1.4.rst
+++ b/doc/source/whatsnew/v1.1.4.rst
@@ -14,7 +14,8 @@ including other versions of pandas.
 
 Fixed regressions
 ~~~~~~~~~~~~~~~~~
--
+
+- Regression in :meth:`MultiIndex.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`36915`)
 
 .. ---------------------------------------------------------------------------
 
diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index a157fdfdde447..6a621d78f266d 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -3468,6 +3468,8 @@ def intersection(self, other, sort=False):
         other, result_names = self._convert_can_do_setop(other)
 
         if self.equals(other):
+            if self.has_duplicates:
+                return self.unique()
             return self
 
         if not is_object_dtype(other.dtype):
@@ -3486,11 +3488,11 @@ def intersection(self, other, sort=False):
         uniq_tuples = None  # flag whether _inner_indexer was successful
         if self.is_monotonic and other.is_monotonic:
             try:
-                uniq_tuples = self._inner_indexer(lvals, rvals)[0]
+                inner_tuples = self._inner_indexer(lvals, rvals)[0]
                 sort = False  # uniq_tuples is already sorted
             except TypeError:
                 pass
-
+        uniq_tuples = algos.unique(inner_tuples)
         if uniq_tuples is None:
             other_uniq = set(rvals)
             seen = set()
diff --git a/pandas/tests/indexes/multi/test_setops.py b/pandas/tests/indexes/multi/test_setops.py
index 6d4928547cad1..121cbe1716b10 100644
--- a/pandas/tests/indexes/multi/test_setops.py
+++ b/pandas/tests/indexes/multi/test_setops.py
@@ -376,3 +376,17 @@ def test_setops_disallow_true(method):
 
     with pytest.raises(ValueError, match="The 'sort' keyword only takes"):
         getattr(idx1, method)(idx2, sort=True)
+
+
+@pytest.mark.parametrize(
+    "tuples", [[("val1", "test1")], [("val1", "test1"), ("val1", "test1")]]
+)
+def test_intersect_with_duplicates(tuples):
+    # GH: 36915
+    left = pd.MultiIndex.from_tuples(tuples, names=["first", "second"])
+    right = pd.MultiIndex.from_tuples(
+        [("val1", "test1"), ("val1", "test1")], names=["first", "second"]
+    )
+    result = left.intersection(right)
+    expected = pd.MultiIndex.from_tuples([("val1", "test1")], names=["first", "second"])
+    tm.assert_index_equal(result, expected)

From fbd63f2d8c2ffd976f4fbc6369b36d8d50af27a5 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Tue, 6 Oct 2020 22:33:38 +0200
Subject: [PATCH 02/20] Fix duplicates in index intersection

---
 pandas/core/indexes/base.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index 4967e13a9855a..905f74b5c20a1 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -2746,7 +2746,7 @@ def intersection(self, other, sort=False):
         self._assert_can_do_setop(other)
         other = ensure_index(other)
 
-        if self.equals(other):
+        if self.equals(other) and not self.has_duplicates:
             return self._get_reconciled_name_object(other)
 
         if not is_dtype_equal(self.dtype, other.dtype):
@@ -2764,6 +2764,7 @@ def intersection(self, other, sort=False):
             except TypeError:
                 pass
             else:
+                result = algos.unique1d(result)
                 return self._wrap_setop_result(other, result)
 
         try:
@@ -2775,7 +2776,7 @@ def intersection(self, other, sort=False):
             indexer = algos.unique1d(Index(rvals).get_indexer_non_unique(lvals)[0])
             indexer = indexer[indexer != -1]
 
-        taken = other.take(indexer)
+        taken = other.take(indexer).unique()
         res_name = get_op_result_name(self, other)
 
         if sort is None:

From 53a37d11716983dc6c65b35989ccf7476a948e30 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Tue, 6 Oct 2020 22:39:41 +0200
Subject: [PATCH 03/20] Modify test and avoid None issues

---
 pandas/core/indexes/multi.py              |  4 +++-
 pandas/tests/indexes/multi/test_setops.py | 17 +++++++++++++----
 2 files changed, 16 insertions(+), 5 deletions(-)

diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index 6a621d78f266d..c62d2a4491327 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -3492,7 +3492,9 @@ def intersection(self, other, sort=False):
                 sort = False  # uniq_tuples is already sorted
             except TypeError:
                 pass
-        uniq_tuples = algos.unique(inner_tuples)
+            else:
+                uniq_tuples = algos.unique(inner_tuples)
+
         if uniq_tuples is None:
             other_uniq = set(rvals)
             seen = set()
diff --git a/pandas/tests/indexes/multi/test_setops.py b/pandas/tests/indexes/multi/test_setops.py
index 121cbe1716b10..f084e76668793 100644
--- a/pandas/tests/indexes/multi/test_setops.py
+++ b/pandas/tests/indexes/multi/test_setops.py
@@ -379,14 +379,23 @@ def test_setops_disallow_true(method):
 
 
 @pytest.mark.parametrize(
-    "tuples", [[("val1", "test1")], [("val1", "test1"), ("val1", "test1")]]
+    ("tuples", "exp_tuples"),
+    [
+        ([("val1", "test1")], [("val1", "test1")]),
+        ([("val1", "test1"), ("val1", "test1")], [("val1", "test1")]),
+        (
+            [("val2", "test2"), ("val1", "test1")],
+            [("val2", "test2"), ("val1", "test1")],
+        ),
+    ],
 )
-def test_intersect_with_duplicates(tuples):
+def test_intersect_with_duplicates(tuples, exp_tuples):
     # GH: 36915
     left = pd.MultiIndex.from_tuples(tuples, names=["first", "second"])
     right = pd.MultiIndex.from_tuples(
-        [("val1", "test1"), ("val1", "test1")], names=["first", "second"]
+        [("val1", "test1"), ("val1", "test1"), ("val2", "test2")],
+        names=["first", "second"],
     )
     result = left.intersection(right)
-    expected = pd.MultiIndex.from_tuples([("val1", "test1")], names=["first", "second"])
+    expected = pd.MultiIndex.from_tuples(exp_tuples, names=["first", "second"])
     tm.assert_index_equal(result, expected)

From 5675a4e712b26f7fea199207c73a76e354109a0c Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Tue, 6 Oct 2020 23:17:26 +0200
Subject: [PATCH 04/20] Fix failing test

---
 pandas/tests/indexes/test_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pandas/tests/indexes/test_base.py b/pandas/tests/indexes/test_base.py
index 8db1bcc84bfa6..8bc252bcc1120 100644
--- a/pandas/tests/indexes/test_base.py
+++ b/pandas/tests/indexes/test_base.py
@@ -683,7 +683,7 @@ def test_intersection_monotonic(self, index2, keeps_name, sort):
 
     @pytest.mark.parametrize(
         "index2,expected_arr",
-        [(Index(["B", "D"]), ["B"]), (Index(["B", "D", "A"]), ["A", "B", "A"])],
+        [(Index(["B", "D"]), ["B"]), (Index(["B", "D", "A"]), ["A", "B"])],
     )
     def test_intersection_non_monotonic_non_unique(self, index2, expected_arr, sort):
         # non-monotonic non-unique

From 582c0b9d752326d36da64a066d105add00b25077 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Fri, 9 Oct 2020 09:16:31 +0200
Subject: [PATCH 05/20] Change comment

---
 pandas/core/indexes/multi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index 3da8b1e5da139..9892c7e149de3 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -3494,7 +3494,7 @@ def intersection(self, other, sort=False):
         if self.is_monotonic and other.is_monotonic:
             try:
                 inner_tuples = self._inner_indexer(lvals, rvals)[0]
-                sort = False  # uniq_tuples is already sorted
+                sort = False  # inner_tuples is already sorted
             except TypeError:
                 pass
             else:

From 7805de53a6ff47ca9bb9abb296e3b89246663596 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sun, 11 Oct 2020 22:22:13 +0200
Subject: [PATCH 06/20] Add unique after intersection

---
 pandas/core/ops/__init__.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index ae21f13ea3f49..95a5353cc438b 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -481,7 +481,9 @@ def _should_reindex_frame_op(
         # TODO: any other cases we should handle here?
         cols = left.columns.intersection(right.columns)
 
-        if len(cols) and not (cols.equals(left.columns) and cols.equals(right.columns)):
+        if len(cols) and not (
+            cols.equals(left.columns.unique()) and cols.equals(right.columns.unique())
+        ):
             # TODO: is there a shortcut available when len(cols) == 0?
             return True
 

From 66b519f8a80a66afad5e9b16828061466bbb0446 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sun, 11 Oct 2020 22:49:10 +0200
Subject: [PATCH 07/20] Fix merge bug

---
 pandas/core/indexes/base.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index 7d2c7e7c95dfa..d06f6be7ac73f 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -2757,8 +2757,7 @@ def intersection(self, other, sort=False):
             indexer = algos.unique1d(Index(rvals).get_indexer_non_unique(lvals)[0])
             indexer = indexer[indexer != -1]
 
-        taken = other.take(indexer).unique()
-        res_name = get_op_result_name(self, other)
+        result = other.take(indexer).unique()
 
         if sort is None:
             result = algos.safe_sort(result.values)

From cb1477b246a90f45c0774be4f2f696651936f7a9 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sun, 11 Oct 2020 23:00:35 +0200
Subject: [PATCH 08/20] Add tests and whatsnew

---
 doc/source/whatsnew/v1.1.4.rst      |  1 -
 doc/source/whatsnew/v1.2.0.rst      |  4 +++-
 pandas/tests/indexes/test_setops.py | 10 ++++++++++
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/doc/source/whatsnew/v1.1.4.rst b/doc/source/whatsnew/v1.1.4.rst
index 57604a38bb642..aa2c77da4ee6f 100644
--- a/doc/source/whatsnew/v1.1.4.rst
+++ b/doc/source/whatsnew/v1.1.4.rst
@@ -20,7 +20,6 @@ Fixed regressions
 - Fixed regression in :class:`RollingGroupby` with ``sort=False`` not being respected (:issue:`36889`)
 - Fixed regression in :meth:`Series.astype` converting ``None`` to ``"nan"`` when casting to string (:issue:`36904`)
 - Fixed regression in :class:`RollingGroupby` causing a segmentation fault with Index of dtype object (:issue:`36727`)
-- Regression in :meth:`MultiIndex.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`36915`)
 
 .. ---------------------------------------------------------------------------
 
diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index bd3112403b31b..3cb4f14d13ccd 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -405,7 +405,8 @@ MultiIndex
 
 - Bug in :meth:`DataFrame.xs` when used with :class:`IndexSlice` raises ``TypeError`` with message ``"Expected label or tuple of labels"`` (:issue:`35301`)
 - Bug in :meth:`DataFrame.reset_index` with ``NaT`` values in index raises ``ValueError`` with message ``"cannot convert float NaN to integer"`` (:issue:`36541`)
--
+- Bug in :meth:`MultiIndex.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`36915`)
+
 
 I/O
 ^^^
@@ -485,6 +486,7 @@ Other
 - Fixed metadata propagation in the :class:`Series.dt` and :class:`Series.str` accessors (:issue:`28283`)
 - Bug in :meth:`Index.union` behaving differently depending on whether operand is a :class:`Index` or other list-like (:issue:`36384`)
 - Passing an array with 2 or more dimensions to the :class:`Series` constructor now raises the more specific ``ValueError``, from a bare ``Exception`` previously (:issue:`35744`)
+- Bug in :meth:`Index.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`31326`)
 
 .. ---------------------------------------------------------------------------
 
diff --git a/pandas/tests/indexes/test_setops.py b/pandas/tests/indexes/test_setops.py
index 1a40fe550be61..be54dce4fed26 100644
--- a/pandas/tests/indexes/test_setops.py
+++ b/pandas/tests/indexes/test_setops.py
@@ -95,3 +95,13 @@ def test_union_dtypes(left, right, expected):
     b = pd.Index([], dtype=right)
     result = (a | b).dtype
     assert result == expected
+
+
+@pytest.mark.parametrize("values", [[1, 2, 2, 3], [3, 3]])
+def test_intersection_duplicates(values):
+    # GH: 31326
+    a = pd.Index(values)
+    b = pd.Index([3, 3])
+    result = a.intersection(b)
+    expected = pd.Index([3])
+    tm.assert_index_equal(result, expected)

From 0fb25612cc66c139cbd8d73e2ec0d9e13b62fbb5 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Mon, 26 Oct 2020 15:45:25 +0100
Subject: [PATCH 09/20] Add rename

---
 pandas/core/indexes/multi.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pandas/core/indexes/multi.py b/pandas/core/indexes/multi.py
index fe0a9a4e5e629..d545de47d17fa 100644
--- a/pandas/core/indexes/multi.py
+++ b/pandas/core/indexes/multi.py
@@ -3476,7 +3476,7 @@ def intersection(self, other, sort=False):
 
         if self.equals(other):
             if self.has_duplicates:
-                return self.unique()
+                return self.unique().rename(result_names)
             return self.rename(result_names)
 
         if not is_object_dtype(other.dtype):

From 10524fdde24403cf705a57bb6adfe2f3a94c71c6 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Mon, 26 Oct 2020 20:31:42 +0100
Subject: [PATCH 10/20] Fix check in merge operation

---
 pandas/core/reshape/merge.py             | 9 +++++++--
 pandas/tests/reshape/merge/test_merge.py | 2 +-
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/pandas/core/reshape/merge.py b/pandas/core/reshape/merge.py
index 5012be593820e..e5ce30095b710 100644
--- a/pandas/core/reshape/merge.py
+++ b/pandas/core/reshape/merge.py
@@ -1207,7 +1207,9 @@ def _validate_specification(self):
                     raise MergeError("Must pass left_on or left_index=True")
             else:
                 # use the common columns
-                common_cols = self.left.columns.intersection(self.right.columns)
+                left_cols = self.left.columns
+                right_cols = self.right.columns
+                common_cols = left_cols.intersection(right_cols)
                 if len(common_cols) == 0:
                     raise MergeError(
                         "No common columns to perform merge on. "
@@ -1216,7 +1218,10 @@ def _validate_specification(self):
                         f"left_index={self.left_index}, "
                         f"right_index={self.right_index}"
                     )
-                if not common_cols.is_unique:
+                if (
+                    not left_cols.join(common_cols, how="inner").is_unique
+                    or not right_cols.join(common_cols, how="inner").is_unique
+                ):
                     raise MergeError(f"Data columns not unique: {repr(common_cols)}")
                 self.left_on = self.right_on = common_cols
         elif self.on is not None:
diff --git a/pandas/tests/reshape/merge/test_merge.py b/pandas/tests/reshape/merge/test_merge.py
index c4c9b0e516192..e3d1a8bb29984 100644
--- a/pandas/tests/reshape/merge/test_merge.py
+++ b/pandas/tests/reshape/merge/test_merge.py
@@ -741,7 +741,7 @@ def test_overlapping_columns_error_message(self):
 
         # #2649, #10639
         df2.columns = ["key1", "foo", "foo"]
-        msg = r"Data columns not unique: Index\(\['foo', 'foo'\], dtype='object'\)"
+        msg = r"Data columns not unique: Index\(\['foo'\], dtype='object'\)"
         with pytest.raises(MergeError, match=msg):
             merge(df, df2)
 

From 3dde0eef56f4f6b2b83c47af577c56001cbb1229 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Thu, 12 Nov 2020 12:51:42 +0100
Subject: [PATCH 11/20] Exit set ops when nonunique

---
 pandas/core/ops/__init__.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index fa4fff46196b0..d024709feac25 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -307,13 +307,14 @@ def should_reindex_frame_op(
     if not isinstance(right, ABCDataFrame):
         return False
 
+    if not left.columns.is_unique or not right.columns.is_unique:
+        return False
+
     if fill_value is None and level is None and axis is default_axis:
         # TODO: any other cases we should handle here?
         cols = left.columns.intersection(right.columns)
 
-        if len(cols) and not (
-            cols.equals(left.columns.unique()) and cols.equals(right.columns.unique())
-        ):
+        if len(cols) and not (cols.equals(left.columns) and cols.equals(right.columns)):
             # TODO: is there a shortcut available when len(cols) == 0?
             return True
 

From d71a499770ec03a987640f78ee2d370d538d9691 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sun, 22 Nov 2020 01:19:13 +0100
Subject: [PATCH 12/20] Roll back to initial version

---
 pandas/core/ops/__init__.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index d024709feac25..fa4fff46196b0 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -307,14 +307,13 @@ def should_reindex_frame_op(
     if not isinstance(right, ABCDataFrame):
         return False
 
-    if not left.columns.is_unique or not right.columns.is_unique:
-        return False
-
     if fill_value is None and level is None and axis is default_axis:
         # TODO: any other cases we should handle here?
         cols = left.columns.intersection(right.columns)
 
-        if len(cols) and not (cols.equals(left.columns) and cols.equals(right.columns)):
+        if len(cols) and not (
+            cols.equals(left.columns.unique()) and cols.equals(right.columns.unique())
+        ):
             # TODO: is there a shortcut available when len(cols) == 0?
             return True
 

From d873d5a849868e3f4bee85a59263d3f07fd54fb7 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sun, 22 Nov 2020 21:35:44 +0100
Subject: [PATCH 13/20] Change whatsnew

---
 doc/source/whatsnew/v1.2.0.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index c20fa0e5a4bb9..dbce8ffa7a415 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -627,7 +627,7 @@ MultiIndex
 - Bug in :meth:`DataFrame.reset_index` with ``NaT`` values in index raises ``ValueError`` with message ``"cannot convert float NaN to integer"`` (:issue:`36541`)
 - Bug in :meth:`DataFrame.combine_first` when used with :class:`MultiIndex` containing string and ``NaN`` values raises ``TypeError`` (:issue:`36562`)
 - Bug in :meth:`MultiIndex.drop` dropped ``NaN`` values when non existing key was given as input (:issue:`18853`)
-- Bug in :meth:`MultiIndex.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`36915`)
+- Bug in :meth:`MultiIndex.intersection` returning duplicates when at least one of the indexes had duplicates (:issue:`36915`)
 
 I/O
 ^^^
@@ -749,7 +749,7 @@ Other
 - Passing an array with 2 or more dimensions to the :class:`Series` constructor now raises the more specific ``ValueError``, from a bare ``Exception`` previously (:issue:`35744`)
 - Bug in ``accessor.DirNamesMixin``, where ``dir(obj)`` wouldn't show attributes defined on the instance (:issue:`37173`).
 - Bug in :meth:`Series.nunique` with ``dropna=True`` was returning incorrect results when both ``NA`` and ``None`` missing values were present (:issue:`37566`)
-- Bug in :meth:`Index.intersection` returned duplicates when at least one of the indexes had duplicates (:issue:`31326`)
+- Bug in :meth:`Index.intersection` returning duplicates when at least one of the indexes had duplicates (:issue:`31326`)
 
 .. ---------------------------------------------------------------------------
 

From e90239ad526d24d8f51a080ac1f8bcfc973ab9eb Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Fri, 27 Nov 2020 19:28:21 +0100
Subject: [PATCH 14/20] Move whatsnew

---
 doc/source/whatsnew/v1.1.5.rst | 2 +-
 doc/source/whatsnew/v1.2.0.rst | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/source/whatsnew/v1.1.5.rst b/doc/source/whatsnew/v1.1.5.rst
index 323342cb43950..d003063b062a7 100644
--- a/doc/source/whatsnew/v1.1.5.rst
+++ b/doc/source/whatsnew/v1.1.5.rst
@@ -17,7 +17,7 @@ Fixed regressions
 - Regression in addition of a timedelta-like scalar to a :class:`DatetimeIndex` raising incorrectly (:issue:`37295`)
 - Fixed regression in :meth:`Series.groupby` raising when the :class:`Index` of the :class:`Series` had a tuple as its name (:issue:`37755`)
 - Fixed regression in :meth:`DataFrame.loc` and :meth:`Series.loc` for ``__setitem__`` when one-dimensional tuple was given to select from :class:`MultiIndex` (:issue:`37711`)
--
+- Fixed regression in :meth:`MultiIndex.intersection` returning duplicates when at least one of the indexes had duplicates (:issue:`36915`)
 
 .. ---------------------------------------------------------------------------
 
diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index dbce8ffa7a415..7ce9cfc7e9ec4 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -627,7 +627,6 @@ MultiIndex
 - Bug in :meth:`DataFrame.reset_index` with ``NaT`` values in index raises ``ValueError`` with message ``"cannot convert float NaN to integer"`` (:issue:`36541`)
 - Bug in :meth:`DataFrame.combine_first` when used with :class:`MultiIndex` containing string and ``NaN`` values raises ``TypeError`` (:issue:`36562`)
 - Bug in :meth:`MultiIndex.drop` dropped ``NaN`` values when non existing key was given as input (:issue:`18853`)
-- Bug in :meth:`MultiIndex.intersection` returning duplicates when at least one of the indexes had duplicates (:issue:`36915`)
 
 I/O
 ^^^

From 742716e5c68b44b9718f3903830615ee7635ac23 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Fri, 27 Nov 2020 19:30:46 +0100
Subject: [PATCH 15/20] Change gh reference

---
 pandas/tests/indexes/multi/test_setops.py | 2 +-
 pandas/tests/indexes/test_setops.py       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pandas/tests/indexes/multi/test_setops.py b/pandas/tests/indexes/multi/test_setops.py
index 0c07f9c64c12d..e1185f6b1ba27 100644
--- a/pandas/tests/indexes/multi/test_setops.py
+++ b/pandas/tests/indexes/multi/test_setops.py
@@ -392,7 +392,7 @@ def test_setops_disallow_true(method):
     ],
 )
 def test_intersect_with_duplicates(tuples, exp_tuples):
-    # GH: 36915
+    # GH#36915
     left = pd.MultiIndex.from_tuples(tuples, names=["first", "second"])
     right = pd.MultiIndex.from_tuples(
         [("val1", "test1"), ("val1", "test1"), ("val2", "test2")],
diff --git a/pandas/tests/indexes/test_setops.py b/pandas/tests/indexes/test_setops.py
index 659fba6f9cf72..2675c4569a8e9 100644
--- a/pandas/tests/indexes/test_setops.py
+++ b/pandas/tests/indexes/test_setops.py
@@ -122,7 +122,7 @@ def test_dunder_inplace_setops_deprecated(index):
 
 @pytest.mark.parametrize("values", [[1, 2, 2, 3], [3, 3]])
 def test_intersection_duplicates(values):
-    # GH: 31326
+    # GH#31326
     a = pd.Index(values)
     b = pd.Index([3, 3])
     result = a.intersection(b)

From 321797a50d349f05f8a6686c51925df83e3f0fae Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Fri, 27 Nov 2020 19:31:38 +0100
Subject: [PATCH 16/20] Remove pd

---
 pandas/tests/indexes/multi/test_setops.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pandas/tests/indexes/multi/test_setops.py b/pandas/tests/indexes/multi/test_setops.py
index e1185f6b1ba27..2ac57f1befd57 100644
--- a/pandas/tests/indexes/multi/test_setops.py
+++ b/pandas/tests/indexes/multi/test_setops.py
@@ -393,11 +393,11 @@ def test_setops_disallow_true(method):
 )
 def test_intersect_with_duplicates(tuples, exp_tuples):
     # GH#36915
-    left = pd.MultiIndex.from_tuples(tuples, names=["first", "second"])
-    right = pd.MultiIndex.from_tuples(
+    left = MultiIndex.from_tuples(tuples, names=["first", "second"])
+    right = MultiIndex.from_tuples(
         [("val1", "test1"), ("val1", "test1"), ("val2", "test2")],
         names=["first", "second"],
     )
     result = left.intersection(right)
-    expected = pd.MultiIndex.from_tuples(exp_tuples, names=["first", "second"])
+    expected = MultiIndex.from_tuples(exp_tuples, names=["first", "second"])
     tm.assert_index_equal(result, expected)

From a980ec08067bd7ec8a862bcbf086b47d4fd36987 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sat, 28 Nov 2020 18:51:45 +0100
Subject: [PATCH 17/20] Remove whatsnew from 1.2

---
 doc/source/whatsnew/v1.2.0.rst | 1 -
 1 file changed, 1 deletion(-)

diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index b4af305383737..049ccc0e6c4df 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -774,7 +774,6 @@ Other
 - Passing an array with 2 or more dimensions to the :class:`Series` constructor now raises the more specific ``ValueError`` rather than a bare ``Exception`` (:issue:`35744`)
 - Bug in ``dir`` where ``dir(obj)`` wouldn't show attributes defined on the instance for pandas objects (:issue:`37173`)
 - Bug in :meth:`RangeIndex.difference` returning :class:`Int64Index` in some cases where it should return :class:`RangeIndex` (:issue:`38028`)
-- Bug in :meth:`Index.intersection` returning duplicates when at least one of the indexes had duplicates (:issue:`31326`)
 
 .. ---------------------------------------------------------------------------
 

From 972fd482931d8257760f8b55752037db0b6f03c0 Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sat, 28 Nov 2020 18:53:03 +0100
Subject: [PATCH 18/20] Fix test

---
 pandas/tests/indexes/base_class/test_setops.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pandas/tests/indexes/base_class/test_setops.py b/pandas/tests/indexes/base_class/test_setops.py
index 6413b110dff2e..ddcb3c5b87ebc 100644
--- a/pandas/tests/indexes/base_class/test_setops.py
+++ b/pandas/tests/indexes/base_class/test_setops.py
@@ -141,7 +141,7 @@ def test_intersection_str_dates(self, sort):
 
     @pytest.mark.parametrize(
         "index2,expected_arr",
-        [(Index(["B", "D"]), ["B"]), (Index(["B", "D", "A"]), ["A", "B", "A"])],
+        [(Index(["B", "D"]), ["B"]), (Index(["B", "D", "A"]), ["A", "B"])],
     )
     def test_intersection_non_monotonic_non_unique(self, index2, expected_arr, sort):
         # non-monotonic non-unique

From fe1ded42428b7df0948fcc08b1ee7555bb31004c Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sat, 28 Nov 2020 19:27:49 +0100
Subject: [PATCH 19/20] Make condition more clear and add assert

---
 pandas/core/indexes/base.py | 6 ++++--
 pandas/core/ops/__init__.py | 7 ++++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index 503d0543ede28..fd82e0efce85e 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -2847,8 +2847,7 @@ def _intersection(self, other, sort=False):
             except TypeError:
                 pass
             else:
-                result = algos.unique1d(result)
-                return result
+                return algos.unique1d(result)
 
         try:
             indexer = Index(rvals).get_indexer(lvals)
@@ -2864,6 +2863,9 @@ def _intersection(self, other, sort=False):
         if sort is None:
             result = algos.safe_sort(result)
 
+        # Intersection has to be unique
+        assert np.array_equal(algos.unique(result), result)
+
         return result
 
     def difference(self, other, sort=None):
diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index fa4fff46196b0..d8b5dba424cbf 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -311,9 +311,10 @@ def should_reindex_frame_op(
         # TODO: any other cases we should handle here?
         cols = left.columns.intersection(right.columns)
 
-        if len(cols) and not (
-            cols.equals(left.columns.unique()) and cols.equals(right.columns.unique())
-        ):
+        # Intersection is always unique so we have to check the unique columns
+        left_uniques = left.columns.unique()
+        right_uniques = right.columns.unique()
+        if len(cols) and not (cols.equals(left_uniques) and cols.equals(right_uniques)):
             # TODO: is there a shortcut available when len(cols) == 0?
             return True
 

From 8e4d47b7a4bcba35f2f947823bdb67c5e53af94e Mon Sep 17 00:00:00 2001
From: phofl <patrick_hoefler@gmx.net>
Date: Sat, 28 Nov 2020 21:01:58 +0100
Subject: [PATCH 20/20] Use shape for equality check

---
 pandas/core/indexes/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index fd82e0efce85e..f746f7a8adbca 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -2864,7 +2864,7 @@ def _intersection(self, other, sort=False):
             result = algos.safe_sort(result)
 
         # Intersection has to be unique
-        assert np.array_equal(algos.unique(result), result)
+        assert algos.unique(result).shape == result.shape
 
         return result