You gotta watch out for your fighter if you let the AI fly it.
What I think happened is that I was accidentally strafed by a patrol ship during a fight with a Wanted NPC. Happens all the time, really. My computer said I was "under attack", even though I wasn't really being attacked (no red enemies on the HUD). But my AI fighter pilot apparently took offense and began firing on the patrol ships. You can guess what happened next... I don't think I made it out of that one, and rebuy on an Anaconda that's probably worth close to half a billion credits is a bitch.
On the flip side, you also have to be careful letting the AI fly your main ship, since they start tinkering with the power distributor settings, and immediately take all the pips out of shields. My shields aren't quite A-rated anyway, and I need at least two pips at all times when I'm in combat. I think next time I might try setting the distributor the way I want, then turning it completely off (basically "locking" the distributor to whatever you set it to, I do the same thing when I'm out exploring) and then switching to the fighter.