BUG-24212 fix usage of Index.take in pd.merge

doc/source/whatsnew/v0.24.0.rst

@@ -1815,6 +1815,7 @@ Reshaping
 - Bug in :func:`DataFrame.unstack` where a ``ValueError`` was raised when unstacking timezone aware values (:issue:`18338`)
 - Bug in :func:`DataFrame.stack` where timezone aware values were converted to timezone naive values (:issue:`19420`)
 - Bug in :func:`merge_asof` where a ``TypeError`` was raised when ``by_col`` were timezone aware values (:issue:`21184`)
+- Bug in :func:`merge` when merging by index name would sometimes result in an incorrectly numbered index (:issue:`24212`)
 
 .. _whatsnew_0240.bug_fixes.sparse:
 

pandas/core/reshape/merge.py

@@ -758,12 +758,26 @@ def _get_join_info(self):
             if self.right_index:
                 if len(self.left) > 0:
                     join_index = self.left.index.take(left_indexer)
+                    if (self.how == 'right' and -1 in left_indexer
+                            and not isinstance(self.right.index, MultiIndex)):
+                        join_list = join_index.to_numpy()
+                        absent = left_indexer == -1
+                        join_list[absent] = self.right.index.to_numpy()[absent]
+                        join_index = Index(join_list, dtype=join_index.dtype,
+                                           name=join_index.name)
                 else:
                     join_index = self.right.index.take(right_indexer)
                     left_indexer = np.array([-1] * len(join_index))
             elif self.left_index:
                 if len(self.right) > 0:
                     join_index = self.right.index.take(right_indexer)
+                    if (self.how == 'left' and -1 in right_indexer
+                            and not isinstance(self.left.index, MultiIndex)):
+                        join_list = join_index.to_numpy()
+                        absent = right_indexer == -1
+                        join_list[absent] = self.left.index.to_numpy()[absent]
+                        join_index = Index(join_list, dtype=join_index.dtype,
+                                           name=join_index.name)
                 else:
                     join_index = self.left.index.take(left_indexer)
                     right_indexer = np.array([-1] * len(join_index))

pandas/tests/reshape/merge/test_merge.py

@@ -1102,6 +1102,16 @@ def test_merge_incompat_dtypes_error(self, df1_vals, df2_vals):
         with pytest.raises(ValueError, match=msg):
             pd.merge(df2, df1, on=['A'])
 
+    def test_merge_on_index_with_more_values(self):  # GH 24212
+        df1 = pd.DataFrame([[1, 2], [2, 4], [3, 6], [4, 8]],
+                           columns=['a', 'b'])
+        df2 = pd.DataFrame([[3, 30], [4, 40]],
+                           columns=['a', 'c'])
+        df1.set_index('a', drop=False, inplace=True)
+        df2.set_index('a', inplace=True)
+        result = pd.merge(df1, df2, left_index=True, right_on='a', how='left')
+        assert 1 in result.index
+
 
 @pytest.fixture
 def left():