In Balloon Park, it's possible to pass through the top, and just run along the top for the whole race. Obviously that earns it a separate division. The rule needs rewriting, since it's possible to skip both balloons on a "normal" lap, and in fact that's the fastest way.
In Desert Palace, it's possible to do a spindash jump left from a ramp, and go so high that you pass over the lap marker without it decrementing a lap, then pass right to get a lap added, repeating for the whole race.
Endless Mine doesn't have a rule yet because I'm not sure what causes it. xebra (aka Ghost), a former member that doesn't come here anymore, made a demonstration video doing something with Tails that caused half a lap to be skipped by moving from the foreground into the background out of nowhere.