Like I said, we need information, without it we can’t help you.
As it turns out you actually have two custom factions fighting each other, with custom ships and npcs, inside a custom system, etc.
The empathy.ini entries of each faction should contain every other faction but not itself!
vignetteparams.ini defines which factions offer which mission types like assassinate, destroy base, …
Additional things I found in old posts:
-The factions should be hostile to each other in initialworld.ini
-Both factions should be spawned in the mission area, as some missions need friendly ships.
Things you can try:
Look at FLSpew
Scan with FLScan II
Replace things with known working ones to narrow down the error(factions/systems/bases/npcs…)