To be clear, this is how I think we got into this state: We have worktrees that are created to squash and rebase a branch. They were left around inadvertently for one reason or another.
Since we were using git v2.14.3, a git gc would prune dangling objects because it never saw that a worktree still had a reference to it. Now, in git v2.15+, worktrees are examined, and a git gc won't garbage collect any objects referenced by a worktree. Another words, the failure of git v2.14 to preserve these objects caused problems with these stale worktrees with the upgrade to v2.15+.
