mypy sometimes emits fewer errors when running on multiple files at once

Bug Report

Hello there,

I am witnessing (rare) cases where mypy emits fewer errors when running on multiple files at the same time than when running on each file individually.

More specifically, I noticed that mypy can fail to report an error when an import for a submodule is missing a one file but present in another file.

I failed to find anything relevant in the documentation or in the existing issues, so I thought I'd let you know. Below is my attempt at a minimal reproducible example.

To Reproduce

(Since multiple files are needed, here is an archive with the reproduction case: repro.zip)

Given a module mymodule with nested modules a and b, and this file foo.py:

import mymodule.a


def blah() -> None:
    mymodule.b.fn()


blah()

As expected, when called on foo.py, mypy emits an error:

$ mypy --cache-dir /dev/null foo.py
foo.py:5: error: Module has no attribute "b"
Found 1 error in 1 file (checked 1 source file)

yet if I add to mypy's command line a second file which does import mymodule.b, say bar.py:

import mymodule.b

then mypy does not emit the error any more, even though I would expect it to:

$ mypy --cache-dir /dev/null foo.py bar.py
Success: no issues found in 2 source files

Your Environment

I used mypy 0.991 on Ubuntu 22.04 with python 3.10.6; I can reproduce this behavior with master, as well as python 3.8, and older versions of mypy.

Unpack repro.zip and run the two commands from the report with foo.py and bar.py to reproduce the differing diagnostics. Trace how imports of mymodule.a and mymodule.b are handled when files are checked together, then ensure the missing-attribute error remains reported in both invocations.