The one that always comes to my mind is the TNG episode "The Next Phase." Geordi and Ro are in a transporter accident and are "out of phase", so they can do stuff like run through walls, people, whatever.
And as soon as I saw that, I was like, "...but why don't they fall through the floor???"

A few months after that Rick Berman was at a con here in Detroit, and I asked about that during his Q & A. He just kind of laughed and said, "Next..."