Often, you can go through the hatches on the floor which you must stomp through without going into them. If you stomp right next to the hatch and move towards it, you will sometimes fall through. It's easiest to try with with the non-X-marked hatches that require holding an item and drilling it through. Hold the object or enemy and drill with it right next to the hatch. Then, move towards the hatch. Wario will still be standing above the hatch but it will go to the cut-scene where Wario is flying through he air. Or, you will just go through the hatch while it's closed.