Did they happen recently though? I ran into a known issue on R3.0, where the filesystem became readonly after too many snapshots. This was fixable simply by booting a newer kernel once (and deleting some old snapshots so it wouldn't happen again right away on the old kernel). But since R3.1 it's been smooth sailing.
Maybe I've just been lucky. I've used btrfs exclusively, starting - before switching to Qubes - when it was still marked "experimental", and never lost any data, AFAIK.
The installer really does its best to hide the automatic btrfs setup option. (Ironically, it was more visible in R3.0, when it wasn't quite ready IMHO.) But once you've bypassed that weird installer bug, you only have to select "btrfs" and then "Click here to create them automatically", that's it!
Hmm... how do you prevent bad backups (with silently corrupted data) from gradually replacing all the good backups?