Starting in World 3, some Boom-Booms will fly around after being stomped once, hoping to swoop down on Mario. If Mario is positioned above Boom-Boom when he pauses right before his swoop attack, Boom-Boom could fly through the ceiling and never return. Since you have to beat Boom-Boom to clear the fortress, Mario will be stuck in the room until time runs out.

The timing is a bit tricky with just Raccoon Mario, so you might want to try using a P-Wing, staying above Boom-Boom until he attacks (duck and fly). You can also get Boom-Boom to hover for the rest of the battle if you're lined up with him when he pauses in mid-air.