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: While still unsure where and when they are, the Nimitz has two F-14 Tomcats aloft, investigating a pair of low-altitude radar contacts. They determine the planes are WWII-vintage Japanese Zeros in full military livery. The Tomcats are told to shadow the Zeros without engaging them. Then, the Captain, the XO, the CAG and Lasky all go to a formal dining room and sit down to tea. In this scene, they talk about many other 1941-era things that are happening, but nobody mentions the Zeros. That fact, and that they left their Tomcats where they did, suggests this scene was meant to be in an earlier part of the film (when things seemed odd, but no imminent threat existed) and got moved here, creating a plot hole that the USS Nimitz could slide through sideways. US Navy nuclear carrier command staff wouldn't simply go have tea under the current conditions. (00:40:30)
