Goofs

(at around 52 mins) When Clark and Lois are talking while she is getting dressed after her shower in their hotel room, shots with only Clark show him with slicked down hair and wearing glasses with smaller lenses, whereas two-shots with Lois and Clark show him with large-lenses and bushy hair.

If time is turned back and everything, starting with Lois' discovery never actually happened, then Clark never would have encountered Rocky in the diner and his "retribution" scene wouldn't make any sense.

(at around 1h 12 mins) When Lex Luthor sits behind the Presidents' desk and lights a cigar while he talks to Zod and company, the cigar switches hands from shot to shot.

(at around 29 mins) When Lex and Miss Tessmacher are in the balloon, after she helps him escape prison, he threatens to punch Miss Tessmacher in the mouth. He makes a fist with one hand, but in the next cut, it's his other hand that has the fist made.

(at around 1h 6 mins) When Clark is lying on the diner floor, he angrily throws the cloth Lois gave him, then rises to confront the bully. In the next cut as Clark stands up he still has the cloth and throws it a second time.

(at around 8 mins) After escaping the Phantom Zone, Zod screams and it echoes. However, as space is a vacuum, the scream not only wouldn't have echoed, but wouldn't have made noise at all.

(at around 1h 6 mins) A goof pointed out in the diner is incorrect. Clark does slam the towel down, but he never let's go of it. So yes. He is still holding the towel when he stands back up.

An obvious stand-in when Clark peeks out of the window down to Lois after he just saved her from suicide.

(at around 26 mins) In the prison scene when Lex Luthor rounds a corner and grabs Otis, the wall they are standing in front of moves when Otis bumps into it.

(at around 1h 23 mins) The scene in Richard Lester's Superman II (1980) where the people on the street are watching Supes and Zod, where the "No Entry" sign is in reverse (flipped film), is still the same in the Donner Cut, contrary to previously published reports.

(at around 1h 24 mins) In Superman (1978), there is a scene where Supes is flying in front of the Twin Towers when he sees the police shootout on the pier. This shot is reused in "S2-the Donner Cut", during the Super Battle. However, the film is flipped so he is flying left to right, instead of right to left (Superman's 'S' is backwards, as well as his hair part).

During the scenes of the Kryptonian villains flying around Metropolis during the Super Battle, and when they fly with Lois and Lex in tow toward the Fortress Of Solitude, you can see the cityscapes through them, and the mountains through Non when he has Lois on his back.

Lex Luthor's "navigation device" he was using on the hot air balloon is simply a JVC multi-band portable radio with a faux rotating "radar" dish attached.

(at around 1h 45 mins) During the sequence where Superman reverses time there are several crowd shots which clearly show modern day New York instead of when the rest of the movie takes place. You can tell by the style of clothes and the cars in the background.

(at around 1h 45 mins) In her final scene, Lois Lane uses an Underwood-Olivetti manual typewriter that sounds like an IBM Selectric.

(At around 45 minutes in) During the hotel scene, a boom mic shadow can be seen in the left corner when Lois mentions how Clark is always gone when Superman arrives.

It makes no sense for Clark Kent to admit to being Superman when Lois Lane shoots him with a blank. Just because he is impervious to bullets doesn't mean he doesn't notice their impact on his body, or in this case, the lack thereof. Also he has X-ray vision and should have noticed it was a blank in the gun.

Superman turns back time so that General Zod, Ursa and Non never leave the Phantom Zone, but we aren't shown how Superman deals with the missiles launched at the end of the first Superman movie - meaning, after turning back time, they should escape again, if Superman dealt with the nuclear missiles in the same manner. (This is a problem that actually stems from the first movie, where we aren't shown Superman dealing with the crisis in a different fashion after Lois dies - he shows up at Lois' car, and the aftershocks that caused her death just never happen.)

The next scene we see is meant to be the beginning of the movie again, with the Daily Planet - so after the nuclear explosions, and before the arrival of the villains - but Clark goes back to straighten out the trucker who hit him afterwards - though because Superman turned back time, basically, this event never happened - so Clark was hitting an innocent man for no reason. (The diner owner says that he just had the place fixed up - meaning the scuffle did occur, and Clark claims he's been working out, meaning from the last time they saw him, when he was beaten - however, again, this never happened because Superman turned back time again.)

Moreover, towards the end of the film, Superman destroys the Fortress of Solitude with his heat-sight - the Fortress of Solitude should be reconstructed (and with Jor-El available to guide Kal-El again) due to Superman turning back time again. The time travel device, beyond complicating the film's time-line, nullifies Jor-El's sacrifice and Superman's lesson, as after turning back time, things should be "back to normal" again.

Furthermore, if Superman's end-game was to turn back time all along, he didn't have to fight the super-villains in Metropolis or in the Fortress of Solitude at all - he could have turned back time immediately after regaining his powers, or following the Metropolis fight.