I was testing 2 drones fleets. One as Pirate and the other as Trade Guild. Pirate got defeated but I was surprise to see fight still occures.
In fact some heat headed Trading Drone focused one of their own team and fight him. They were all against that one for an obscure reason.
Friendly fire was ON though, so the focused drone took damage.
Fact also this drone got some close range weapons (pulse damage type), so I suppose while attacking the last pirate target the pack was condensed and hit each other with the pulse damage weapon set. So the guy may have shutted down the shield from one of his ally and then get focused by them (I had noticed neutral AI auto-activate as aggressive mode when their shield are down by another neutral target).
Friendly fire was on though, so the focused drone took damage.
MISSILE_DEFENSE_FRIENDLY_FIRE = true
That thing happened few minutes before I left and close server. There are numerous logs (but just last one should help, and seems that something spammed logs too so I don't know if it'll be usefull)