BUG: Fix inconsistent pivot table subaggregation when index is None

doc/source/whatsnew/v3.0.0.rst

@@ -665,6 +665,7 @@ Reshaping
 - Bug in :meth:`DataFrame.join` when a :class:`DataFrame` with a :class:`MultiIndex` would raise an ``AssertionError`` when :attr:`MultiIndex.names` contained ``None``. (:issue:`58721`)
 - Bug in :meth:`DataFrame.merge` where merging on a column containing only ``NaN`` values resulted in an out-of-bounds array access (:issue:`59421`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when ``sort=False`` (:issue:`54987`, :issue:`55516`)
+- Bug in :meth:`DataFrame.pivot_table` incorrectly subaggregating results when called without an ``index`` argument (:issue:`58722`)
 - Bug in :meth:`DataFrame.unstack` producing incorrect results when manipulating empty :class:`DataFrame` with an :class:`ExtentionDtype` (:issue:`59123`)
 
 Sparse

pandas/core/reshape/pivot.py

@@ -557,7 +557,12 @@ def _all_key(key):
                 table_pieces.append(piece)
                 margin_keys.append(all_key)
         else:
-            from pandas import DataFrame
+            margin = (
+                data[cols[:1] + values]
+                .groupby(cols[:1], observed=observed)
+                .agg(aggfunc, **kwargs)
+                .T
+            )
 
             cat_axis = 0
             for key, piece in table.groupby(level=0, observed=observed):
@@ -566,9 +571,7 @@ def _all_key(key):
                 else:
                     all_key = margins_name
                 table_pieces.append(piece)
-                # GH31016 this is to calculate margin for each group, and assign
-                # corresponded key as index
-                transformed_piece = DataFrame(piece.apply(aggfunc, **kwargs)).T
+                transformed_piece = margin[key].to_frame().T
                 if isinstance(piece.index, MultiIndex):
                     # We are adding an empty level
                     transformed_piece.index = MultiIndex.from_tuples(

pandas/tests/reshape/test_pivot.py

@@ -2785,3 +2785,31 @@ def test_pivot_empty_with_datetime(self):
             index="category", columns="value", values="timestamp"
         )
         assert df_pivoted.empty
+
+    def test_pivot_margins_with_none_index(self):
+        # GH#58722
+        df = DataFrame(
+            {
+                "x": [1, 1, 2],
+                "y": [3, 3, 4],
+                "z": [5, 5, 6],
+                "w": [7, 8, 9],
+            }
+        )
+        result = df.pivot_table(
+            index=None,
+            columns=["y", "z"],
+            values="w",
+            margins=True,
+            aggfunc="count",
+        )
+        expected = DataFrame(
+            [[2, 2, 1, 1]],
+            index=["w"],
+            columns=MultiIndex(
+                levels=[[3, 4], [5, 6, "All"]],
+                codes=[[0, 0, 1, 1], [0, 2, 1, 2]],
+                names=["y", "z"],
+            ),
+        )
+        tm.assert_frame_equal(result, expected)