I am missing something about these missions. I took one mission in a system, it said to kill 12 citizens of that faction, but all the settlements that faction owns are abandoned or are military bases who are not citizens. What am I missing?
The faction was in a negative state and the settlements abandoned. There was a mismatch between the mission and the situation on the ground. Is the faction present in any other systems?
I don't think the mission server knows if the target faction is under states which causes the settlements to be abandoned. So you may have taken an impossible mission.