Here is the situation. I was running through my latest mission after publishing it. Near the end of it, there is a point where there are some space battles. After the battle finishes, an NPC contact ship is supposed to become active near the battle site.
The problem is the point at which the last ship died just happened to be pretty much on top of where the NPC contact ship is supposed to turn active. So when the warp core breach happened it destroyed the NPC contact ship.
Now, my mission didn't require an objective to actually talk to the contact, however I can imagine it is possible that this kind of thing could happen in someone elses mission where you were intended to actually talk to the contact that gets destroyed in such a freak accident, and would thus stop the mission from being completed.
There are a few issues here, first and foremost, this was an issue because contacts spawn at level 1, but the mission was being run at level 51 with a Lt General. If the contact was my level, the warp core breach likely would only have scratched the paint. Second, a contact should just be indestructible anyways since we can't do anything to make them hostile.