Revealing mistake: When Jor-El is placing the baby Kal-El into the spacecraft, you can see his Rolex under his sleeve.
Visible crew/equipment: Just after young Clark Kent jumps in front of the train, there is a close up of the train speeding by with a very visible camera in its reflection.
Continuity mistake: Kal-El's cradle arrives on earth, flies zooming past the Kents' car, which is driving in the opposite direction and crashes 500 meters behind the vehicle. The car keeps moving for about 200 meters and then pulls over. A brief shot shows an intact curb on the right. However, when Jonathan Kent gets out of the car, everything changes: The cradle has moved 700 meters and lays next to the car; and the immaculate field is now destroyed by a huge ditch.
Plot hole: After Superman has reversed time the Hoover Dam reverts to its previous undamaged state as it should, but Jimmy Olsen should then have been replaced back on the dam. Instead he interrupts the potential kiss between Lois and Superman and complains of being abandoned by Superman in the desert.
Continuity mistake: When leaving the Daily Planet for the first time together Clark gets stuck in the revolving door behind Lois. He lets her go through ahead of him and gets in the next section as the door revolves. Cut to the exterior of the Planet when they emerge (just before they meet Rex Reed) and Clark is in the same section of the revolving door as Lois.
Visible crew/equipment: Near the beginning when Lois and Clark are walking out of the Daily Planet, Clark gets stuck in the revolving doors. But, look closely at the glass door, and you can see Richard Donner (confirmed in Superman expanded commentary) holding the door so that Christopher Reeve can get stuck.
Revealing mistake: In the shot of Krypton exploding, you can see creases in the black backdrop in the lower, left hand quadrant of the screen (especially visible on Blu-Ray).
Other mistake: When the camera pulls back from Superman in his Fortress of Solitude, right after the image of his father wanting to hug him disappears, you can see on the right of the screen that one of Superman's 'crystal' walls is fluttering or shaking like it's made of plastic.
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.
Continuity mistake: After Superman saves the train from derailing, there's a wide shot of the lead locomotive and it has just one small window on the side. In the immediate close-up there's a big window where the conductor peeps, and a sudden second window with a handle bar where another engineer shows up.