BUG: values argument ignored when also supplied to index/columns in pivot_table

[it176131]

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• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

import numpy as np
import pandas as pd
from pandas import Index, MultiIndex
import pandas.testing as tm


def test_pivot_table_values_in_columns():
    """``values`` arg is shared between ``values`` and ``columns``."""
    data = [
        ["A", 1, 50, -1],
        ["B", 1, 100, -2],
        ["A", 2, 100, -2],
        ["B", 2, 200, -4],
    ]
    df = pd.DataFrame(data=data, columns=["index", "col", "value", "extra"])
    result = df.pivot_table(values="value", index="index", columns=["col", "value"])
    nan = np.nan
    e_data = [
        [50.0, nan, 100.0, nan],
        [nan, 100.0, nan, 200.0],
    ]
    e_index = Index(data=["A", "B"], name="index")
    e_cols = MultiIndex.from_arrays(
        arrays=[[1, 1, 2, 2], [50, 100, 100, 200]], names=["col", "value"]
    )
    expected = pd.DataFrame(data=e_data, index=e_index, columns=e_cols)
    tm.assert_frame_equal(left=result, right=expected)


def test_pivot_table_values_in_index():
    """``values`` arg is shared between ``values`` and ``index``."""
    data = [
        ["A", 1, 50, -1],
        ["B", 1, 100, -2],
        ["A", 2, 100, -2],
        ["B", 2, 200, -4],
    ]
    df = pd.DataFrame(data=data, columns=["index", "col", "value", "extra"])
    result = df.pivot_table(values="value", index=["index", "value"], columns="col")
    nan = np.nan
    e_data = [
        [50.0, nan],
        [nan, 100.0],
        [100.0, nan],
        [nan, 200.0],
    ]
    e_index = MultiIndex.from_arrays(
        arrays=[["A", "A", "B", "B"], [50, 100, 100, 200]], names=["index", "value"]
    )
    e_cols = Index(data=[1, 2], name="col")
    expected = pd.DataFrame(data=e_data, index=e_index, columns=e_cols)
    tm.assert_frame_equal(left=result, right=expected)


test_pivot_table_values_in_columns()  # Fails.
test_pivot_table_values_in_index()  # Fails.

Issue Description

When the column supplied to values in pandas.DataFrame.pivot_table is also supplied to index or columns, the resulting DataFrame does not contain the aggregations of the values argument. If any extra column(s) are present, those columns are aggregated instead of those supplied to values. This is similar to issue #57876, but the additional columns result in a non-empty DataFrame.

Expected Behavior

I would expect the two tests above to pass, i.e., the values arg is aggregated instead of the non-supplied "extra" column.

# Expected output of ``test_pivot_table_values_in_columns``:
col       1             2       
value   50     100    100    200
index                           
A      50.0    NaN  100.0    NaN
B       NaN  100.0    NaN  200.0

# Expected output of ``test_pivot_table_values_in_index``:
col              1      2
index value              
A     50      50.0    NaN
      100      NaN  100.0
B     100    100.0    NaN
      200      NaN  200.0

Installed Versions

INSTALLED VERSIONS

commit : 0691c5c
python : 3.13.3
python-bits : 64
OS : Windows
OS-release : 11
Version : 10.0.22631
machine : AMD64
processor : AMD64 Family 25 Model 116 Stepping 1, AuthenticAMD
byteorder : little
LC_ALL : None
LANG : None
LOCALE : English_United States.1252

pandas : 2.2.3
numpy : 2.2.4
pytz : 2025.2
dateutil : 2.9.0.post0
pip : 25.0.1
Cython : None
sphinx : None
IPython : 9.1.0
adbc-driver-postgresql: None
adbc-driver-sqlite : None
bs4 : 4.13.3
blosc : None
bottleneck : None
dataframe-api-compat : None
fastparquet : None
fsspec : None
html5lib : None
hypothesis : None
gcsfs : None
jinja2 : 3.1.6
lxml.etree : None
matplotlib : None
numba : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
psycopg2 : None
pymysql : None
pyarrow : None
pyreadstat : None
pytest : 8.3.5
python-calamine : None
pyxlsb : None
s3fs : None
scipy : 1.15.2
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlsxwriter : None
zstandard : None
tzdata : 2025.2
qtpy : None
pyqt5 : None