Audio problem: When Non is launched towards the Empire State a man says "Wow, home run!", but his lips are not in sync.
Plot hole: Lois Lane and other people see Clark Kent unhurt when a taxi hits him and suffers damage, but don't draw the obvious conclusion that there's something extraordinary about him.
Suggested correction: I always took this as an intentional jab at how the people of Metropolis, and Lois in particular, were so oblivious to the fact that Clark was obviously Superman. Still a plot hole, just an intentional one.
Suggested correction: Maybe the cab-driver thinks that Clark is extraordinary, but he is shocked in the first moment, worrying about his damaged car. Later than he realises that this guy is maybe Superman, but cannot find him anymore. Just a guy of millions walking around the big apple.
Continuity mistake: Inside the White House the cops fire 3 or 4 times at Zod but the wall and statue behind him have at least 15 bullet holes.

Other mistake: When the elevator explodes there's a shot of the Phantom Zone and Ursa is a totally different actress. Different to the other unknown actress used on the first movie, which is also listed as a mistake.
Continuity mistake: Right after Clark reveals himself to Lois in Niagara Falls hotel room, by his hand falling into the fire, he backs up to where the bed and lava lamp like column is behind him. In that shot, there isn't much of the "lava" in the column. The scene cuts to a shot of Lois and then back to Clark and suddenly there is a lot of "lava" in the column. (00:53:05)

Continuity mistake: In the diner, whilst Clark is asking the bad guy to step outside, the waiter is leaning over the baddie's right shoulder. When the angle changes he is leaning on the left shoulder.
Continuity mistake: When the villains are being judged, for a brief second they change positions, Zod being on the far right instead the far left.
Audio problem: At the Eiffel Tower, after Lois asks the French officer if the terrorists have the proper equipment, his voice is heard but from a side view his mouth and jaw don't move.
Continuity mistake: In East Houston, behind the man lifted by Zod, there's a man standing several feet away from a car. A frame later he's very close to the car.
Continuity mistake: When Zod burns several cars, the street is filled with parked cars and people. From Superman's point of view the street is empty and you only get to see the three burning cars and a couple of cabs.
Audio problem: When the villains blow the people back in Metropolis, all the ones near the KFC restaurant (the waitress, the guy in the phone booth and the couple) shout or make comments but their mouths either don't move or are not in synch.
Revealing mistake: Before the villains change the faces on Mt. Rushmore, the original ones (which are a matte painting) have a greenish look. Definitely not like the real sculptures.
Revealing mistake: At the beginning of the movie, we see the three villains in front of several backgrounds. In most of these backgrounds, their outlines are fuzzy, indicating that they are actually standing in front of a green screen.
Visible crew/equipment: When the super baddies arrive on the moon and encounter the astronauts, the girl Kryptonian kicks one of the astronauts into space and you can see the strings around his waist as he floats away.
Other mistake: The phantom zone villains were captured and put in space near Krypton. When Kal-El was sent to Earth, he has to pass 6 galaxies to arrive (his father said, before Krypton exploded). When Superman sends the hydrogen bomb in Paris into space, he didn't even leave the solar system. No way the phantom zone travelled through 6 galaxies - it has no propulsion, and the shock wave from the bomb wouldn't travel that far either.
Revealing mistake: When Zod jumps out of Perry's window he falls down, revealing its a stunt from a ground level window. The outside shots however, show Zod flying up and straight.
Continuity mistake: After Superman crushes Zod's hand, his hair gets wet and the fringe appears combed as a toupee.
Continuity mistake: When Ursa is moving the helicopter around, the sky keeps changing from sunny to cloudy.
Deliberate mistake: Luthor and Teschmaker visit the North Pole protecting themselves against the cold. Lois manages to wander around with a mere, but sexy, shirt.