I had a noticed several times the NPC's where asking me to destroy their own ships.
6 players. Me and 5 NPC. 3 Loyalists and 3 Rebels
Me + 2 Loyalists and the other 3 where Rebels.
I was trying to woo another loyalist and he wanted me to kill his own ships seemed like all the time.
I also noticed the others seemed to be offering self targeted missions but as I can't say how often as I was more or less ignoring them