This is a rather minor bug, but I noticed upon finishing the game that even though I retook the Black Crawler base for the Zone Rats with Gorsky, Sneaky, and Dan--and did it with no casualties--the ending slide for Core City gives me the following line, which shouldn't play because Dan joined the Zone Rats and survived:
EDIT: Uh, okay for some reason 2/3rds of my post just got deleted. It looked fine when I posted it, but whatever. What I was saying was that the ending slide for the Zone Rats played as if Dan never joined the Zone Rats, which he did in my playthrough. I assume that the flag for Dan joining the Zone Rats and living wasn't checked off for some reason.