This bug was originally reported in the helix repository: helix-editor/helix#12604
I was doing a bit of a research in that issue, and I found that helix is using the package ignore, and we can see instances of WalkBuilder in the file picker function here.
The full explanation of the bug can be read there, but the TLDR is: if the global .gitignore, specified in git's config core.excludesfile option contains a rooted pattern, for example /.venv, it is not ignored as expected.
I looked for similar issues to see if anyone have reported it already, but I was unable to find any.