There certainly are cases with well-understood causes (e.g. birds flew into both engines to make them stop), but I guess there are cases that originally caused from combination of previously-unknown failure pattern; since the failure pattern understood enough to write a software to detect, it may likely be backed up by some fail-safe mechanism.

I don't know much about aircraft controlling software, so this is only a guess from my experience of general system software crash recovery; usually the hardest case is caused by something I've never imagined to happen.