Tracked files are sometimes incorrectly shown as modified in `git status` output

Occasionally, tracked files are incorrectly shown as modified in `git status` output.

A closely related issue is git-lfs/git-lfs#1726. The "fix" described in the initial comment seems to work with the git-crypt version of the issue as well. As far as I can tell, however, (as that issue thread is very long), no fix was ever committed for it.

Interestingly, in a state where `git status` erroneously shows files as changed, different git clients exhibit different behavior when checking the status. For example, the error is not seen in Sublime Merge, but it is still in Git Cola.