Was trying to find a scientific explanation, but the best I was able to find basically chalked up a lot of what was wrong with the time travel scene to bad writing.
Especially since he supposedly stopped the second missile after traveling back in time thus saving Lois since the earthquake never made it to her stalled car hinting that it never happened, and yet both Lois and Jimmy (who's conveniently near enough to her car to join in on this scene for more face time) still mention the Gas Station exploding and earthquakes, and massive destruction that was only a direct result of the missile hitting the fault line, which Superman supposedly had gone back in time to stop. Which means, he didn't stop the missile, it still hit, and the earthquake still happened. So how/why did that earthquake never reach Lois' car? It was never explained and makes for something of a paradox... Unless Superman has some new power that was never mentioned anywhere, he can't simply "stop" earthquakes, so what happened here...? If he didn't stop the missile despite going back in time, why not? He had the ability to... And if he didn't stop the missile, then how did he stop the earthquake exactly? The whole thing doesn't make any sort of sense.
As far as the other Paradox, of there being two Supermen due to the second timeline's never needing to go back since Lois was still alive, I suppose that could be solved with Professor's Farnsworth's explanations in Futurama on multiple timeline's versions of the same person existing in the same timeline(Not directly related to Superman, I know, but it's a reasonable theory considering the other Superman is never seen or mentioned...), and the universe automagically fixed itself by somehow killing off that timeline's Superman(Maybe some kind of massive Kryptonian heart attack from lifting up the entire several million tons of dirt and rocks at the faultline earlier during the initial attempts to stave off the destruction?) leaving the Lois is dead Superman to continue to exist as the only one.
Largely though, I think this two part video explains rather effectively how many issues there were with Superman in all 5 movies(Superman through to Superman Returns...), mostly focusing on his unreasonable stupidity...
Superman is a moron: Part 1Superman is a moron: Part 2Suffice to say, bad writing aside, these two videos cite some pretty good examples of how Superman did quite a few less than intelligent things in his various movie outings, screwing with time travel/the earth's rotation being only one of them. One of their rather good examples from the third movie was when he was welding a hole in the side of an oil tanker with heat vision while very flammable oil is just on the other side of that hole. Sure he wouldn't be hurt by the explosion, but everyone on the ship would die(and realistically, should have when the whole thing should have exploded), and that's not very Paragon of him, to borrow a quote from Goku in Dragonball Z Abridged...
In fact, Superman on several occasions in all five films(Again, not counting The Man of Steel, especially since I haven't seen it just yet, so I can't speak for that one...) does things that make no sense from the perspective of him being the supposed "altruistic" hero he's always depicted as in comics and cartoons. Like leaving a large airplane parked in the middle of a baseball stadium and leaving it up to someone else to figure out how to get it out, or casually dropping a very large boat on the street in front of a police station once again leaving someone else to figure out what to do with it, or putting the Daily Planet's globe down on someone's car completely crushing it, or like when he takes Lois flying in the first movie and then decides in a brilliant move to let go of her and simply watch as she plummets a good few hundred feet before he catches up and catches her (which let's be honest, any normal person would've considered that a bit of a d*** move and held it against him, even if he did catch them afterwords... Personally, if I were Lois, I wouldn't care how "hot" the man was, he was still an a** for doing that...), or...
Well, you get the idea... It's pretty obvious, unfortunately, that Hollywood's vision of Superman is that he's a bit more of a jerk of an alien who does what ever he pleases without ever stopping to consider the consequences than he should be, even if he does occasionally save cats from trees and always saves Lois just in time... Well, except that one time, in California, during that earthquake where he didn't quite make it in time... But that never happened... *Brain explodes*