I think the two missiles struck, more or less, simultaneously, so Superman could only stop one. As EzraS notes, he stopped the one headed towards Hackensack New Jersey because he promised Eve Teschmacher that he would, because her mother lived in Hackensack and Superman always keeps his promises.
The other missile did, indeed, hit the San Andreas fault and triggered an earthquake with accompanying disasters — bridge collapse, dam burst, train almost derailing, Lois Lane dying. When Superman reversed time, he undid the disasters — it's been a while since I watched the film, but I distinctly remember the water flowing back into the broken dam and the dam itself reforming. So, while the second missile still hit, it did no damage thanks to Superman. He even created a tornado by flying around the explosion at super speed to suck the mushroom cloud and accompanying radiation out into space.
Incidentally, in the original script, the first missile — the one headed towards Hackensack — which Superman sent off into space was going to hit the Phantom Zone prison square and release Zod and co. When the filmmakers decided to turn that script into two movies, the bomb in the Eiffel Tower was created to free the Phantom Zone prisoners instead.