Not OP, but I've encountered a few situations where the solution was modifying .git/ manually. The one that comes to mind was having two branches with names separated only by case on a case sensitive system, and then checking out both on a case insensitive system.
It's been awhile so my memory is fuzzy, but this was at a windows-only shop back before WSL was a thing and getting a VM involved an annoying months-long requisition process. I think the repo state was actually corrupted too, so pull may not have been working.
