These may be unique to the Super-mythos, but similar problems crop up all the time in every show; not just the science fiction/fantasy category. And it's supposed to be the job here at Toobworld Central to find the splainins for these discrepancies.
Luckily, it seems Ken has had quite a few responses to the questions he raised, such as how could Superman fly a little girl around the world in three hours without burning her to a crisp?
But the one that always puzzles me was first brought to my attention in a Robert Wuhl monologue - Why is it that Superman has no problems when the bad guys shoot bullets at him, but he always ducks when they throw their guns at him?
Go read Ken Levine's entry, as well as its follow-up, "Superman II". Good stuff!
"One does not thank logic."