Crashing to Desktop (CTD) both during Space Combat and while attempting to "Leave" it is definitely a widespread bug. Yet another case of releasing content well before it is ready.
As for proton torpedoes... They share lock-on with regular missiles. So, all you need to do is have one missile target come between you and your torpedo target and BAM, you've lost your target acquisition. It has always been complained about but (shocker) nothing has been done.