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• 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

mi1 = pd.MultiIndex.from_tuples([(1, pd.NA)])
mi2 = pd.MultiIndex.from_tuples([(1, 1), (1, 2)])

mi2.isin(mi1)

Issue Description

output:

array([True, True])    # <- main
array([False, False])  # <- 1.5.0

Regression is on main only and looks to be a result of #48622.

The bug is not in MultiIndex.isin per se, but #48622 looks to have exposed the underlying bug to MultiIndex.isin.

Open PR #48877 will fix the underlying bug.

Expected Behavior

array([False, False])

Installed Versions