Plot hole: Lois and a friend of hers are watching Non and Superman fight. But this is totally senseless, because Superman had been flying around Metropolis and chances are slim that he appears in the very same spot to let Lois watch him. And, second and most important, should any doubts arise, the panning angles of the camera never show Lois's building, with the big broken window and the flag poles.
Plot hole: When Superman becomes human for Lois, the molecule chamber nearly rips him apart, he suffers. At the end of the movie, when he tricks out of the evil 3 and turn them into humans with the same radiation, they are just looking around, wondering about the strange lights, but don't suffer at all.
Suggested correction: Well it's established that Superman has altered the machine. Maybe he also reprogrammed it to not leave signs of their powers being removed.
Plot hole: Lois Lane and other people see Clark Kent unhurt when a taxi hits him and suffers damage, but don't draw the obvious conclusion that there's something extraordinary about him.
Suggested correction: I always took this as an intentional jab at how the people of Metropolis, and Lois in particular, were so oblivious to the fact that Clark was obviously Superman. Still a plot hole, just an intentional one.
Suggested correction: Maybe the cab-driver thinks that Clark is extraordinary, but he is shocked in the first moment, worrying about his damaged car. Later than he realises that this guy is maybe Superman, but cannot find him anymore. Just a guy of millions walking around the big apple.
