I actually had this happen once when I was running a small filesystem based git server. Users could login with normal shell sessions with their public key, and repo permissions were handled with the unix permissions system. Some user with a funky git UI client for windows actually deleted a repo completely from the server.
It wasn't much of an issue because of local copies, but we moved to git-shell right after that, and to gitlab not long after when then team grew beyond a handful of people.
It's Git either way, how does code get lost? It's not centralized unless you don't trust your local copies.