In mission 3 of the prologue, if you get shot down by one of the pirates while trying to torpedo the frigate(Pretty likely considering Alpha 1 provides no cover whatsoever) the mission will go to the normal victory debriefing and you'll be able to proceed. Getting shot down anywhere else has no unexpected results, you just die. I don't remember if there used to be a special debriefing for getting shot down in that exact point, but it's a pretty weird bug. Occurred on both RC2 and a recent nightly.
I'd attach a log, but getting to that point in the mission on a debug build would be pretty hard considering how much it whines all the time.
EDIT: same thing in the 7th mission of the main campaign(Vega 2), getting killed while trying to defend fort crocket leads to a "mission won" briefing and you're able to continue.