Plot hole: After Superman has reversed time the Hoover Dam reverts to its previous undamaged state as it should, but Jimmy Olsen should then have been replaced back on the dam. Instead he interrupts the potential kiss between Lois and Superman and complains of being abandoned by Superman in the desert.
Plot hole: Superman could have easily caught both missiles, proven by how fast we see him flying around the globe just a few minutes later. He's fast enough to circle the globe multiple times in seconds, but struggles for minutes to catch the missile.
Plot hole: When there is a big explosion at a plant and Superman flies in to save the day, all he does to stop the explosions is pull down the toggle of a huge switch situated on the wall; if this is all that was needed to stop the explosions, then why didn't one of the workers do it, and save Superman the trouble of flying all the way out there to do something which one of the workers could have done easily.