On the level where you race the rat to diffuse the bomb, sometimes the game doesn't move you onto the stage boss when you boot the last bomb. This is unfortunate because there is no way out of this other than to reset. I had a theory that this glitch was caused by the game being confused as to who actually got to the bomb first when it's a "tie". One day, I saw what really happens to cause it. I was watching the rat drop down the floors as he normally does when he suddenly went right through the wall on the right side of the screen and disappeared! I could still hear the sound of him bumping around, but he was nowhere to be seen. When you boot the bomb, the rat is supposed to fall down and hit his head on the floor, which shakes the screen and causes you to fall down to where the boss is. But since the rat had disappeard, he couldn't fall, and he couldn't shake the screen, thus leaving the toad stranded at the end of the level.
Taken with permission from Flying Omelette.