local stubs folder makes mypy think an unrelated module.__init__ duplicates module

[Avasam]

Bug Report

Having a local stubs folder makes mypy think an unrelated module.__init__ duplicates module.

Deleting the __init__.pyi in the local stubs solves the issue, but will cause many more issues where mypy thinks the package can't be imported.

This happens with or without explicit_package_bases.

To Reproduce

MRE: reproduction.zip

Expected Behavior

No error or some way to work around this issue

Actual Behavior

my_package\_dynamic\__init__.py: error: Source file found twice under different module names: "my_package._dynamic" and "my_package._dynamic.__init__"
my_package\_dynamic\__init__.py: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#mapping-file-paths-to-modules for more info
my_package\_dynamic\__init__.py: note: Common resolutions include: a) adding `__init__.py` somewhere, b) using `--explicit-package-bases` or adjusting MYPYPATH
Found 1 error in 1 file (errors prevented further checking)

Your Environment

• Mypy version used: mypy 1.15.0 (compiled: yes)
• Mypy command-line flags: python3.13 -m mypy .
• Mypy configuration options from mypy.ini (and other config files): (see MRE)
• Python version used: Python 3.13.0