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It's quite common in comics (and elsewhere, I suppose) to portray castles and other such stone structures as having stone floors thru-out, but, unless I am missing something, stone floors would be possible only on the lowest level, the one where the floor is actually laid down on solid ground. Above that, on second, third, etc floors, or on balconies (such as Doom is standing on), there would be nothing underneath to support the massive weight of the stone, so wooden flooring would be used.

(This is a mistake I used to make myself from time to time. I seem to recall a shot in FF where She-Hulk is crashing up thru the floor to an upper level of Doom's castle, and stone is flying everywhere. Oops!)

It would, of course, be possible to lay a thin veneer of stones on top of a wooden floor, but that would not produce the effect of big blocks of stone flying thru the air when somebody or something bursts up thru the floor.