"git worktree remove" fails if git-annex has operated on the worktree, because git expects .git in a worktree to be a file, while git-annex changes it to a symlink (Using git-worktree with annex). Also, git-annex-test does not currently seem to test git-annex operation on worktrees added by git-worktree?
This seems like something the git developers might consider a bug in git worktree, since generally git doesn't care if .git is a symlink or a pointer file.
Although perhaps the reason it checks is to avoid deleting something it didn't set up.
I don't see any way to improve this in git-annex though, if .git is not a symlink then every git-annex symlink in the repository will need to change to point to the real path to .git/annex/objects, which is not practical.
Maybe git considers .git an internal detail, so they might not guarantee things working correctly if it's changed to a symlink? A clean way to handle this would be to add a 'git annex worktree' command, which normally just passes the rest of the command line to 'git worktree', but handles any git-annex-specific details as needed: e.g. 'git annex worktree add' calls 'git worktree add' then replaces the .git pointer file with symlink; 'git annex worktree remove' puts the .git pointer back then calls 'git worktree remove', etc.