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  • [x] I have confirmed this bug exists on the latest version of pandas.

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

Reproducible Example

import pandas as pd

levels1 = ['b', 'a']
levels2 = pd.Index([1, 2, 3, pd.NA], dtype=pd.Int64Dtype())
index = pd.MultiIndex.from_product([levels1, levels2], names=['level1', 'level2'])

df = pd.DataFrame(dict(value=range(len(index))), index=index)
print(df)

print(df.unstack(level='level2'))

print(df.unstack(level='level2', sort=False))
               value
level1 level2
b      1           0
       2           1
       3           2
       <NA>        3
a      1           4
       2           5
       3           6
       <NA>        7
       value
level2  <NA>  1  2  3
level1
a          3  0  1  2
b          7  4  5  6
Traceback (most recent call last):
  File "/home/jared/tmp/./250402-pd-test.py", line 15, in <module>
    print(df.unstack(level='level2', sort=False))
          ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/frame.py", line 9928, in unstack
    result = unstack(self, level, fill_value, sort)
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/reshape/reshape.py", line 504, in unstack
    return _unstack_frame(obj, level, fill_value=fill_value, sort=sort)
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/reshape/reshape.py", line 537, in _unstack_frame
    return unstacker.get_result(
           ~~~~~~~~~~~~~~~~~~~~^
        obj._values, value_columns=obj.columns, fill_value=fill_value
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/reshape/reshape.py", line 242, in get_result
    return self.constructor(
           ~~~~~~~~~~~~~~~~^
        values, index=index, columns=columns, dtype=values.dtype
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/frame.py", line 827, in __init__
    mgr = ndarray_to_mgr(
        data,
    ...<4 lines>...
        typ=manager,
    )
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/internals/construction.py", line 336, in ndarray_to_mgr
    _check_values_indices_shape_match(values, index, columns)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jared/opt/mambaforge/envs/pd-test/lib/python3.13/site-packages/pandas/core/internals/construction.py", line 420, in _check_values_indices_shape_match
    raise ValueError(f"Shape of passed values is {passed}, indices imply {implied}")
ValueError: Shape of passed values is (2, 4), indices imply (2, 5)

Issue Description

With a MultiIndex level of Int64Dtype() containing NA values, DataFrame.unstack() produces the expected result with sort=True (default) but causes an exception with sort=False. This does not occur if the NA value is removed from the index.

Expected Behavior

No exception, the returned DataFrame has level in the original order (['b', 'a']).

Installed Versions

INSTALLED VERSIONS ------------------ commit : 0691c5cf90477d3503834d983f69350f250a6ff7 python : 3.13.2 python-bits : 64 OS : Linux OS-release : 5.15.167.4-microsoft-standard-WSL2 Version : #1 SMP Tue Nov 5 00:21:55 UTC 2024 machine : x86_64 processor : x86_64 byteorder : little LC_ALL : None LANG : C.UTF-8 LOCALE : C.UTF-8 pandas : 2.2.3 numpy : 2.2.4 pytz : 2024.1 dateutil : 2.9.0.post0 pip : 25.0.1 Cython : None sphinx : None IPython : 9.0.2 adbc-driver-postgresql: None adbc-driver-sqlite : None bs4 : None blosc : None bottleneck : None dataframe-api-compat : None fastparquet : None fsspec : None html5lib : None hypothesis : None gcsfs : None jinja2 : None 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 : None python-calamine : None pyxlsb : None s3fs : None scipy : None sqlalchemy : None tables : None tabulate : None xarray : None xlrd : None xlsxwriter : None zstandard : None tzdata : 2025.2 qtpy : None pyqt5 : None

Comment From: gsmll

take

Comment From: snitish

Thanks for reporting. Confirmed on main. PRs to fix are welcome.

Comment From: manemln

take