[BUG]: Fix ValueError in concat() when at least one Index has duplicates

doc/source/whatsnew/v1.2.0.rst

@@ -345,6 +345,7 @@ Reshaping
 - Bug in :func:`union_indexes` where input index names are not preserved in some cases. Affects :func:`concat` and :class:`DataFrame` constructor (:issue:`13475`)
 - Bug in func :meth:`crosstab` when using multiple columns with ``margins=True`` and ``normalize=True`` (:issue:`35144`)
 - Bug in :meth:`DataFrame.agg` with ``func={'name':<FUNC>}`` incorrectly raising ``TypeError`` when ``DataFrame.columns==['Name']`` (:issue:`36212`)
+- Bug in :func:`concat` resulted in a ``ValueError`` when at least one of both inputs had a non unique index (:issue:`36263`)
 -
 
 Sparse

pandas/core/reshape/concat.py

@@ -495,7 +495,19 @@ def get_result(self):
                     # 1-ax to convert BlockManager axis to DataFrame axis
                     obj_labels = obj.axes[1 - ax]
                     if not new_labels.equals(obj_labels):
-                        indexers[ax] = obj_labels.reindex(new_labels)[1]
+                        # We have to remove the duplicates from obj_labels
+                        # in new labels to make them unique, otherwise we would
+                        # duplicate or duplicates again
+                        obj_labels_duplicates = obj_labels[
+                            obj_labels.duplicated()
+                        ].unique()
+                        new_labels_cleared = new_labels[
+                            ~(
+                                new_labels.duplicated()
+                                & new_labels.isin(obj_labels_duplicates)
+                            )
+                        ]
+                        indexers[ax] = obj_labels.reindex(new_labels_cleared)[1]
 
                 mgrs_indexers.append((obj._mgr, indexers))
 

pandas/tests/reshape/test_concat.py

@@ -2927,3 +2927,15 @@ def test_concat_preserves_extension_int64_dtype():
     result = pd.concat([df_a, df_b], ignore_index=True)
     expected = pd.DataFrame({"a": [-1, None], "b": [None, 1]}, dtype="Int64")
     tm.assert_frame_equal(result, expected)
+
+
+def test_concat_duplicate_indexes():
+    # GH 36263 ValueError with non unique indexes
+    df1 = pd.DataFrame([1, 2, 3, 4], index=[0, 1, 1, 4], columns=["a"])
+    df2 = pd.DataFrame([6, 7, 8, 9], index=[0, 0, 1, 3], columns=["b"])
+    result = pd.concat([df1, df2], axis=1)
+    expected = pd.DataFrame(
+        {"a": [1, 1, 2, 3, np.nan, 4], "b": [6, 7, 8, 8, 9, np.nan]},
+        index=pd.Index([0, 0, 1, 1, 3, 4]),
+    )
+    tm.assert_frame_equal(result, expected)