Autons will attack nearby targets, and also react to being attacked.
This results in it being virtually impossible to keep them alive. I regularly have lone autons taking potshots at enemy stations, then going off to fight the station guards alone and getting themselves into trouble. Furthermore, because they react to being fired upon, there is no way to recall them. You can try, but they'll most probably be hit on their way out, and immediately retaliate.
As autons are even more expensive than they otherwise would be what with custom tweaks to them being available in CC, losing an auton to bad AI can be seriously crippling. In my current playthrough I've spent a good 80K or so on autons in one way or another. Nearly all of them are dead through aggravating enemy stations, shooting each other to death when ordering them to attack a target (How do you miss a sung transport from 15ls away?), or blowing each other up with Longreach I's every time something dies (this is mostly down to the ancient problems with missile defense which still plague ICX/longreach devices, which is something for another thread once someone figures out a way to make them work properly).
The easy solution to the basic problem is to make the "form up" order over-ride the defensive reaction. If an auton is being ordered to return home, it will do so.
The underlying issue, however, is that defense reactions don't stop sometimes. If you can provoke a scavenger into annoying a station guard, or vice versa, they will fight to the death, no matter how long it takes (or at least, you could in the release candidates. I have not tried this in 1.2+CC but from what I can tell it should still occur). It's actually incredibly funny to watch, provided you can afford the fuel to wait there for 5-10 minutes. The AI could really do with a "screw it, let's go do something else" switch that stops fights from going on forever (rather than basing things off distance, which doesn't always work) and stops one-off annoyances turning into a desperate chase across the entire sector as two random ships battle to the death over a stray ICX shot.
The problem lies in that the changes to AI allow for long-distance luring of enemies. This is a good thing, and it might be impacted by trying to fix this issue. I'm not entirely sure how that could be dealt with, sadly. AI tweaks are never a simple matter, alas.
