I thought right away that it must have to do with the new BombBot explosions. I was right. It took me a few tries to spot the error though.
I had to look for any clues I could find in the game's behavior. I eventually caught a break, when after blowing up a BombBot, I observed that it also destroyed the remains of a dead RobotGuard. Basically, BombBot explosions were capable of rekilling enemies. So, I quickly fixed it.
I've played through the game twice since, and the bug hasn't occured again, so I'll assume I got it. Just to be safe, I'm going to test it some more before moving on.
I would really like to get back to level design and creating new enemies now. I've got some great ideas for level 3, especially the boss, that I want to try out.
I might release a new demo this weekend.