Unable to unlink old ' xxxx ' in repo. How do I fix?

I have an installation of Gitlab CE upgraded to 12.2.5 recently that we have been using without problems. However, in our CI tests, in one git repo we’ve starting having the problem

error: unable to unlink old `$FILENAME` Permission Denied

where $FILENAME is a list of about 150 fixture files. I"ve checked permissions, and we did have a container reset them to root… I set them back… but I now can’t get the tests running successfully again. Any thoughts on how to fix?