[stubtest] fix duplicate errors with invalid line numbers

[jorenham]

Closes #15023

[jorenham]

I verified that this works by running scipy-stubs==1.16.3.3 against scipy==1.17.0rc1, with a before/after of 714->536 reported stubtest errors.

[jessekrubin]

AHA! This is the commit that is causing me my-mypy woes!

@jorenham @ilevkivskyi I have pybind11 and pyo3 modules where a barrel/__init__.pyi reexports things so as to avoid having a bazillion line line single stub file. Mypy isn't able to import the faux stub modules because they dont exist. For reference, here is one of my public projects that has the aforementioned stub layout:

• project: https://github.com/jessekrubin/ry
• stubs: https://github.com/jessekrubin/ry/tree/main/python/ry/ryo3

Pinning to 1.19.1 works for me, but anything after that is broken. Any recommendations? I would like to keep my broken up stubs.