Bug in concat creating invalid MultiIndex

doc/source/whatsnew/v1.4.0.rst

@@ -261,7 +261,7 @@ Groupby/resample/rolling
 
 Reshaping
 ^^^^^^^^^
--
+- :func:`concat` creating :class:`MultiIndex` with duplicate level entries when concatenating a :class:`DataFrame` with duplicates in :class:`Index` and multiple keys (:issue:`42651`)
 -
 
 Sparse

pandas/core/reshape/concat.py

@@ -717,8 +717,9 @@ def _make_concat_multiindex(indexes, keys, levels=None, names=None) -> MultiInde
         new_levels.extend(new_index.levels)
         new_codes.extend([np.tile(lab, kpieces) for lab in new_index.codes])
     else:
-        new_levels.append(new_index)
-        new_codes.append(np.tile(np.arange(n), kpieces))
+        new_levels.append(new_index.unique())
+        single_codes = new_index.unique().get_indexer(new_index)
+        new_codes.append(np.tile(single_codes, kpieces))
 
     if len(new_names) < len(new_levels):
         new_names.extend(new_index.names)

pandas/tests/reshape/concat/test_dataframe.py

@@ -180,3 +180,15 @@ def test_concat_bool_with_int(self):
         result = concat([df1, df2])
         expected = concat([df1.astype("int64"), df2])
         tm.assert_frame_equal(result, expected)
+
+    def test_concat_duplicates_in_index_with_keys(self):
+        # GH#42651
+        index = [1, 1, 3]
+        data = [1, 2, 3]
+
+        df = DataFrame(data=data, index=index)
+        result = concat([df], keys=["A"], names=["ID", "date"])
+        mi = pd.MultiIndex.from_product([["A"], index], names=["ID", "date"])
+        expected = DataFrame(data=data, index=mi)
+        tm.assert_frame_equal(result, expected)
+        tm.assert_index_equal(result.index.levels[1], Index([1, 3], name="date"))