Unfortunately I don’t have a reproducible test case but very often when I am using sublime as my editor for git commit and such, a git operation will fail with a permission error which if I recall, is because the file is open for exclusive access elsewhere.
This often happens during an interactive rebase which is incredibly annoying because I have to cancel the rebase and try again.
I believe the problem is related to Sublime’s scanning of files that are in the tree on the left side.