diff --git a/packages/@vue/cli/__tests__/Generator.spec.js b/packages/@vue/cli/__tests__/Generator.spec.js
index 77a780cb95..5a97a794d1 100644
--- a/packages/@vue/cli/__tests__/Generator.spec.js
+++ b/packages/@vue/cli/__tests__/Generator.spec.js
@@ -457,6 +457,9 @@ test('api: extendPackage + { prune: true }', async () => {
 
   await generator.generate()
 
+  // should not warn about the null versions
+  expect(logs.warn.length).toBe(0)
+
   const pkg = JSON.parse(fs.readFileSync('/package.json', 'utf-8'))
   expect(pkg).toEqual({
     version: '0.0.0',
diff --git a/packages/@vue/cli/lib/util/mergeDeps.js b/packages/@vue/cli/lib/util/mergeDeps.js
index 410f02f487..d437532cbd 100644
--- a/packages/@vue/cli/lib/util/mergeDeps.js
+++ b/packages/@vue/cli/lib/util/mergeDeps.js
@@ -42,6 +42,7 @@ module.exports = function mergeDeps (
 
     if (prune && injectingRange == null) {
       delete result[depName]
+      continue
     }
 
     if (!isValidRange(injectingRange)) {