I changed a shield in the auton bay on a 300D and ended up with a duplicate auton. Had one with the new shield and still had one which had the old shield. All other items were the same.

Debug output:
OnDestroy [300D defender auton]: Invalid property [autonItem] ### ([email protected] aWreckObj "autonItem" autonItem) ###

Another duplication. Different game.
I was in Domitus with a TX3 and a 300D in the auton bay. Also had a (mod) 770 Mule auton waiting in the Sanctuary system.
I gated back to Sanctuary.
Hit 'Q' then 'F' then 'G' to summon the auton and then gate back to Domitus quickly.

On re-arriving in Domitus I also had an extra TX3 and an extra 300D flying around. They had gated in somehow. The original TX3 and 300D were still in the auton bay.
The armor for the duplicate TX3 was dwarg catoptric not blast plate as in the original. I had previously put damaged dwarg catoptric armor on the TX3 to repair it using the auton bay armor repair feature but it was replaced for blast plate before the first gating to Domitus.
All other items on both duplicate autons were the same.

.sav available. No debug log output.

relanat 16 May 2021:

Some vague info.
I have had numerous duplications but they are rare.
Most seem to occur when gating, another duplicate auton will gate in.
There seems to be a correlation with the auton being in the auton bay repairing its armor, and the duplicate auton will often have an armor that was previously fitted to it although it can also be the currently installed armor too. I frequently put damaged armor on autons to repair it for sale and then refit the desired armor.
Duplicate autons can also have shields that were previously installed but as these do not repair they are not changed as frequently.
Duplicate autons that appear on gating do not produce any debug output.

This suggests that info on the auton in its previous configuration (or duplicate info for an unchanged auton) is not being cleared somehow, so the uncleared info is being used by the gating code and an additional auton is created.