I have a master and a dev branch.
I made commits in both.
I also deleted some files in dev.
I made other commit in master, so this master branch is more recent.
I had the same problem. In my case I think the problem was that, when I did the merge, my copy of the merged-from branch was outdated compared to the remote. (a colleague had done the deletion, not me)
In any case, what fixed it was deleting the whole working copy and cloning it anew.