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.
Suggested correction: Superman had never flown that fast before in the movie. It could be argued that he was still in the process of discovering and pushing the limits of his powers and it was the emotional episode of losing Lois that motivated him to push himself.
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.
Suggested correction: Superman is moving at speeds fast enough to turn back time. He can spend 5 seconds to yank Jimmy away from the top of a dam he knows is going to be destroyed just to be safe in case he can't actually stop it all from happening again.
Plot hole: When Superman goes after the missile that's heading for New Jersey he leaves Metropolis (which is actually New York City). He would have met the missile head on, but he appears to catch up to the missile from behind and while it's still over territory somewhere around the Grand Canyon, so he probably could have stopped both missiles before the second one hit the fault line.