Factual error: Harry stumbles onto his dad's secret room and it is free of dust except for a few cobwebs. While there may have been no human activity in the room for almost two years, there were holes in the room that let sunlight, air, and insects/arachnids in, therefore there must have been airflow. With the airflow, dust or dirt should have entered the room and collected on the items.
Continuity mistake: In the first few shots of Mary Jane held hostage by Dr. Octopus in the factory, her arms above her head change from straight to bent and back.
Character mistake: In the start of the film, the sticker on Peter's head for his work misspells the word Bleecker Street on it.
Continuity mistake: In the train scene, Spider-Man is thrown through a window and the fight continues over the broken window. When a train is coming from the opposite direction, Spider-Man leans over to avoid it, and the window isn't broken anymore.
Revealing mistake: During the final battle, when Spidey tells Doc Ock "we have to give up the thing we want the most... even our dreams", watch the tentacle behind Doc Ock's head. Right after Spidey says "even our dreams", the three "claws" on the tentacle close, and you can see the tip of the bottom "claw" pass through the tip of one of the other claws, revealing a blunder in the rendering of the digital effect. (This is visible in the DVD release of the theatrical cut of the film. It was corrected in the "2.1" edition, and may have been corrected in the Blu-Ray release, but it's still plainly visible on the original DVD release).
Continuity mistake: When the car crashes in the cafe, it crashes against a column on the left. In subsequent shots the column has no damage at all.
Continuity mistake: Mary Jane holds the wedding card with her left hand. A frame later she is holding it with her right hand.
Continuity mistake: When Peter asks Mary if she wants some chop-suey, the same cab passes behind her twice.
Continuity mistake: The chip on Dr. Ock's nape is 10 centimeters away from his hair. In the close-up it's right next to the hair.
Continuity mistake: In the bank, a desk filled with papers zooms towards Dr. Ock. The papers fly away, but reappear a frame later when he tears the table apart.
Continuity mistake: Spidey and Octopus fight at the tower and a huge chunk of concrete falls on the street below. Seconds later, however, cars are seen moving around, no honks, no crashes, no problems at all, as if the falling rubble had simply vanished.
Continuity mistake: Spiderman and Octopus fall on the train carriage's roof and dent it, then roll several carriages back. When the angle changes to an outside view, they are on the third carriage and neither it nor the first two are dented. (01:30:55)
Continuity mistake: When Spider-Man stops the train his head and chest fall forward due to the momentum, but a frame later - from a different angle - he is standing still, his body against the train structure.
Revealing mistake: After Tobey Maguire stops the train, he is stopped from falling by the passengers on the train. As he pulled back into the train, the vertical metal hand rail on the left-hand side bends and shakes like jelly when it is gently touched by the male passenger as he pushes Tobey into the train even though the hand rail is still intact and fixed to the train. This is probably used so Tobey would not be injured while pressing up against the train during the filming of the scene.
Revealing mistake: When Dr. Ock abducts Mary Jane he is replaced by a lame CGI figure.
Visible crew/equipment: Boom mic reflected on upper part of phone when Peter puts a 50 cent coin in.
Visible crew/equipment: When Peter rides his motorbike, in the wide shots he's replaced by an obvious stunt double who wears safety goggles.
Visible crew/equipment: Film crew and boom mic reflected on lower left glass of cafe when Dr. Ock approaches.
Deliberate mistake: Perhaps to avoid getting an R rating or parental complaints notice how in the operating room massacre none of the doctors appear to bleed nor do Doc Ock's tentacles have blood on them.
Suggested correction: The problem is in both versions of the film, basically all of the deaths either happen off-camera, or are things like people being shocked to death or killed by being tossed around and presumably having their backs/necks broken. Most of the deaths would be bloodless or near-bloodless anyways, and the camera simply doesn't linger on the bodies enough to show any blood. This is also why the tentacles aren't really bloody. Sure, it was probably ratings-related, but it isn't technically a mistake.
Deliberate mistake: When Doc Ock is robbing the bank, there are two close-ups showing his claws shovelling cash into tan-coloured bags. In the first close-up, you can plainly see the shot is mirrored, as all the text on the bags is mirrored. It also conspicuously seems to have the exact same plastic baggie and small stack of cash next to it as the second shot. It looks like it's two different takes of the same shot, and they mirrored one to make it look like a different shot.
