A few months ago, I moved to Linux Mint 14 “nadia”, which is based on Ubuntu 12.10 “quantal quetzal”. I sometimes see this error after running a commmand with sudo:
rm: cannot remove `/run/user/root/gvfs': Is a directory
This happens because the root user has started a gvfsd daemon, which mounts a virtual filesystem on that directory. The root user should never run GNOME, so it should never need gvfsd. But something in Ubuntu 12.10 starts one sometimes.