Glad reverting back solved your situation.
There's always one sleeping molerat at Starlight. In the ground, northside between the screen and the shack. If you come down the hill at the right angle you can pick it up in VATS and see that it is not hostile yet (green target). Unlike the other molerats (who are always hostile), it won't aggro until you get near it and wake it up. I suspect this is why the civilians in prebuilts don't just go ahead and kill it like the others. They can't/don't wake it/aggro it. Then, if left to slumber, it somehow gets counted as a civilian when you schedule an attack. Same principle btw for the (two) sleeping ghouls in the cabin with the magazine at Sunshine.
It's important to scout out both Starlight and Sunshine (at least enough to wake up the sleeping baddies) prior to launching an assault. This solves the problem on the front end.