BUG: sort_index on a multiindex changes values of the index

[erezinman]

Pandas version checks

• I have checked that this issue has not already been reported.

• 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
import numpy as np
idx = pd.MultiIndex(levels=[['a', 'b', 'c'], [16., 32., 4.]], codes=[[0, 1, 2, 2], [-1, -1, 1, 1]])
df = pd.DataFrame(np.arange(16).reshape(4, 4), columns=idx)
df
#     a   b    c     
#   NaN NaN 32.0 32.0
# 0   0   1    2    3
# 1   4   5    6    7
# 2   8   9   10   11
# 3  12  13   14   15

df.sort_index(axis=1)

#      a    b    c     
#   4.0  4.0  32.0 32.0
# 0    0    1    2    3
# 1    4    5    6    7
# 2    8    9   10   11

Issue Description

The empty values are filled with values that shouldn't be there.

Expected Behavior

The value in the first and second column index after sorting should be np.nan but instead it's filled with 4.0. This is quite severe!

Installed Versions

INSTALLED VERSIONS

commit : 2e218d1
python : 3.9.12.final.0
python-bits : 64
OS : Linux
OS-release : 5.4.0-139-generic
Version : #156-Ubuntu SMP Fri Jan 20 17:27:18 UTC 2023
machine : x86_64
processor : x86_64
byteorder : little
LC_ALL : None
LANG : en_US.UTF-8
LOCALE : en_US.UTF-8
pandas : 1.5.3
numpy : 1.22.0
pytz : 2022.1
dateutil : 2.8.2
setuptools : 61.2.0
pip : 22.3.1
Cython : 0.29.30
pytest : 7.1.2
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : 3.1.2
IPython : 8.5.0
pandas_datareader: None
bs4 : 4.11.1
bottleneck : 1.3.5
brotli :
fastparquet : None
fsspec : 2022.11.0
gcsfs : None
matplotlib : 3.6.2
numba : 0.56.0
numexpr : 2.8.4
odfpy : None
openpyxl : 3.0.10
pandas_gbq : None
pyarrow : 6.0.1
pyreadstat : None
pyxlsb : None
s3fs : None
scipy : 1.7.3
snappy : None
sqlalchemy : 1.4.27
tables : 3.7.0
tabulate : 0.8.10
xarray : 2022.10.0
xlrd : 2.0.1
xlwt : None
zstandard : None
tzdata : None

[erezinman]

Sorry, this is probably the same as #25818. Didn't check well enough before. Regardless, I think mine is a simpler MWE if you want to use it.

[phofl]

No worries, closing as duplicate. Can you post your example there as well?