BUG: Fix duplicates in intersection of multiindexes

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`)
 
 .. ---------------------------------------------------------------------------
 

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):
@@ -3486,10 +3488,12 @@ 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
+            else:
+                uniq_tuples = algos.unique(inner_tuples)
 
         if uniq_tuples is None:
             other_uniq = set(rvals)

pandas/tests/indexes/multi/test_setops.py

@@ -376,3 +376,26 @@ 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", "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, exp_tuples):
+    # GH: 36915
+    left = pd.MultiIndex.from_tuples(tuples, names=["first", "second"])
+    right = pd.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"])
+    tm.assert_index_equal(result, expected)