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.
Visible crew/equipment: Boom mic reflected on upper part of phone when Peter puts a 50 cent coin in.
Revealing mistake: When Dr. Ock abducts Mary Jane he is replaced by a lame CGI figure.
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.
Visible crew/equipment: When Peter rides his motorbike, in the wide shots he's replaced by an obvious stunt double who wears safety goggles.
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.
Visible crew/equipment: Film crew and boom mic reflected on lower left glass of cafe when Dr. Ock approaches.
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.
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.
Other mistake: During the hospital scene where the robotic arms kill all the operating room staff, we see 4 different camera angles on the last doctor to be killed. All the arms have cameras in them, and show his face screaming at 4 different angles. Yet it should only be 3 as one arm has its claw wrapped around his neck. And it doesn't release from him, as it can be seen still wrapped around his neck by the other 3 cameras in each claw.
Visible crew/equipment: The camera and a boom mic are visible in the police car lights in the scene directly following the first accident with Doc Ock.
Continuity mistake: When Spidey faints after stopping the train he is carried away by the passengers. One of them raises her right arm to help. A shot later her arm is lowered, and she is raising it again. (01:36:00)
Continuity mistake: Right before Spidey stops the train there's a lot of people inside next to him. Then a wide shot later they've vanished only to reappear a shot later.
