Hi,
During 'repo sync' one of the .git repositories got corrupt during the check out phase. A subsequent 'repo sync' command showed no error or warning. Yet, the .git folder was still corrupt. It could be repaired by manually removing the index.lock file inside the .git, and then checking out this .git manually.
My proposal would be to add a check against such situations and at least create a warning.
The .git folder probably got corrupt when I ran a 'du' command from another terminal window on the same location where the repositories were being checked out.