At present, if autons damage a docked ship, or destroy one, the game treats it as if the player did it.
The problem is that autons are as dumb as a brick, and NEVER hold their fire. This leads to easy aggravation, which given that the AI in 1.2 tends to follow autons to the ends of the universe rather than give up (autons retaliate for the attack, causing it to continue, etc), is problematic. It's also REALLY easy to lose access to important stations. With Corporate Command making autons more useful and important, this is extremely problematic for Constellation pilots, who already get to start out in probably the worst starting equipment setup in the game.
I believe a better alternative would be to log damage caused by the player's autons seperately to what the player does, and have them be confronted by the station owners. This results in them being forced to pay for damages, facing court action for repeat offences (fines+potential for a jailing), or being executed by the Syndicate if they really annoy them or can't pay their price after shooting up a black market.
Handling "defensive" attacks against autons could also do with some AI tweaks. At present, a swarm of autons around a ship will ALWAYS result in massive battle if one of them aggros a defender (see above for mechanism. It's a cascade of defensive reactions combined with the terrible aim and fire control that autons have). Making it so that defenders will always break off a chase past a certain distance if their station is still alive, and giving the player a "hold fire!" order to sqaudrons so they can effectively stop them firing *at all* would fix that right up.
