Hmmm... The problem with being in a super secret spy/experimental program is you don't know who your friends are. Trinity sort of knows that Reese and Holly are safe, but the guy chasing her... And even after he rescues her, she still has doubts. She's also convinced she's self-destructing because she's feeling too much. And then there are the headaches, which mysteriously go away after he rescues her.
The other problem with being in a super secret spy/experimental program is the assumption on the part of your "handlers" that the virus/training makes you a mindless drone. So far, the growing band of escapees has been more concerned with a) getting off the grid and b) finding/keeping safe the seemingly random female who strikes their viral fancy. Of course, the people overseeing the program are trying to eliminate the pairs, because the females catch it, and they don't like that any more than they like their toys being distracted. I would guess that at some point in the past, they took out one of the females, and the male went nuts. I would also guess these were the ones that didn't survive induction. But nothing is said about that.
All I know is I'll be real disappointed if a book for Bey doesn't get written.