This may happen if you update the index to ignore certain files:
git update-index --assume-unchanged <file>
and then for instance checkout some other branch:
git checkout <branch>
> error: Entry '<file>' not uptodate. Cannot merge.
Forcing index refresh fixes the issue:
git update-index --really-refresh
<file>: needs update
Followed by:
git reset --hard
And then everything should be back to normal.