I had the following issue in my Project ID ST-TJ8YK9MRY (Mustrum's Combat Simulator):
I created a bunch of Borg NPC groups and then duplicated these. (The duplication part might be important, since this never was a problem before).
Afterwards, I changed the type of enemies behind that group to Klingon NPC groups. In one case, I took a Borg Weak Frigate Group into a Klingon Fighter Group.
The Fighter group has a lot more NPCs in it then the original Borg group. The extra actors did have their position set to an empty position (e.g. X=Y=Z=0). I did such shenanigans before and they never caused issues - but this is the first time I used duplicate. Maybe that is the underlying issue.
I have never seen anything else than the situation you just described. If I know there will be more actor places, I first remove the old squad, then add the new one (which probably results in a bugged objective, so you might have to remove the objective leading to that enemy group as well).