Factual error: When Clark speaks to Jor-El for the first time in the Fortress, Jor-El says "I will have been dead for many thousands of your years..." Fine in theory - Baby Kal-El travelled to Earth at above light speed so time passed differently for him. However, as such, wouldn't Jor-El have seen Earth as it was thousands of years ago? Which also makes there a problem with all the things Kal-El was taught during his voyage to Earth, as Jor-El references Einstein by name, for instance, and he would not have existed at the point when Jor-El sent him to Earth.
Factual error: When Superman is turning back time by flying around the Earth, right before he starts orbiting the Earth is spinning way faster than it actually should be. If the Earth actually spun that fast, a day would pass by every 1.44 minutes.