I've been reassured by that one Star Trek episode where Riker and Ro are out of phase with the rest of the ship that you can never pass through floors, only walls.
I remember a certain episode of batman beyond as a kid giving me a strange fear of "using powers to phase through walls and ending up accidentally falling through the ground". On second thought though, thats the least of your concerns; you wont actually hit the ground or anything and more importantly you'll phase through the air molecules as well instead of breathing them
Gravity plating in the floors! Their phased baryons were able to pass through normal matter, but not through the graviton fields running through all the floors of the decks.
Now don't ask how they were able to breathe, because I've got nothing on that.