On the second prologue mission, where you escort the freighter Aurora, I think I must have missed one of the demons because the freighter exploded pretty quick. My wingmen didn't say anything about its loss, and once we were done killing the pirate fighters in the immediate area I could not autopilot. Off in the distance, perhaps 50k away, was another group of pirate fighters, just sitting there. I afterburned over to them, and they just sat there.
I replayed the mission and killed the demons, and didn't have a problem. I should probably see if I can repeat the mission and let the Aurora die, but I think I'll play a few missions first.
By the way, I'm really loving the destroyable containers on the freighter. It really adds something to the experience to see how much damage it took.