I was fighting bullseye in challenge mode, and I kept knocking him more and more negative. The thing is, the game kept continuing on. What gives?

Someone else mentioned this in another thread too. Apparently it's just a bug in the game.

It's now doing that on all challenge missions. Could it be the fact that I have beat the Hero and Villain modes?

No, just turn the game off and start again, it should be fine. This happen to me as well when I was playing.

I was doing one of the puzzles and it did that. I was at 0 and my opponet was at -1 and it just kept going to next turn. So -213646431354354 END. later...:ermm:

Yeah on my game I can't do any of the chalanges since no matter who I face it doesn't stop at zero. In addition I have tried turning it off then on again like Toe-nee sugested, but it doesn't work.

So I went back to puzzle mode after playing much of the story mode. The puzzle that I previously mentioned was Leader #1. Apparently, I didn't recruit in the specific order needed to beat the puzzle. Yeah, I've fixed that now...