I discovered a problem in git-subtree that I could also reproduce in a minimal proof of concept over at https://github.com/tionis/git-subtree-bug-poc
The same bug was discussed some time ago on stackoverflow: https://stackoverflow.com/questions/68761778/git-subtree-cache-exists
It seems to occur when a subtree was added, removed, alter added again and then modified in some commit.
This leads to some error with the cache leading to an error message like
fatal: cache for $commit-hash-here already exists!
I'm unsure how to work around this other than modify the history or creating a branch from before the first addition and fixing it there.