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: Richard eventually manages to travel back in time by removing all the modern items from his room. But what about the spotlights above his bed? (00:31:40)
Plot hole: When the fog finally hits the lighthouse and is seeping in, the generator is hardly audible vs. how loud it was when it was first started.