I've had this problem for a while now but it's finally driven me mad. I have a directory with some local mercurial repos. I'm the only user who touches these repos.
Things will go fine for a while, and suddenly I'll do a commit and then hg will die with abort: Permission denied: on one of the ./hg/* files. When I look at the file I'll find it's owned by 1000:messagebus. So I'm too busy to investigate so I just "sudo chown -R $USER:users ~/path/to/repo" and go along my way... then the next day—or whenever—the same thing happens again! It's weird because I don't have a user with uid=1000 in /etc/passwd, but messagebus has a gid=1000. Also the seems to only happen to the two Hg repos I am working on. The last time this happened (just now), the mtime on the file is 18 June. The ctime is 19 June (the fs is mounted with noatime). The last time I did the chown thing was on the 20th (so the ctime kinda doesn't make sense, if I understand correctly), so could this possibly be a bug in the fs (ext4)?