It was not hacked or modified, it was dirty. I bought a copy of Super Mario All Stars off of Ebay years ago and it had a bunch of crazy glitches, hit the X button and you would change powers, neat stuff. If I turned it off and back on it was still like what I was describing. I cleaned the cart and it all went away, kinda wish I didn't do that.
So no, hacking the EEPROM and then reprogramming the game using Assembly to randomly mess up would have been a huge waste of time and resources.