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.
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.
Continuity mistake: Spidey throws a huge iron minute hand at Ock which destroys an enormous chunk of concrete and makes loads of debris fall downward. However, a shot later there's a view of the street and the train track and not only is the debris gone from the road but the traffic and people act as if nothing had happened.
Continuity mistake: After the car slams the cafe, Peter watches the street with people running around. The reflection on his lenses has nothing to do with what the opposite angle shows.
Continuity mistake: When Peter/Spider-Man has his first web failure and falls on the pipes on the building's roof, he keeps his hands free in one shot and then his right hand is put on his chest in the next.
Continuity mistake: Kids buying fruit suddenly appear behind Peter when he arrives at the pizza place for the first time.
Continuity mistake: Peter back flips off his moped to avoid the car racing at him. There were cop cars and other vehicles behind that car when Peter jumps, but when he lands only one cop car goes past in the lane next to him and the lane he's standing in is then clear of traffic as he talks to some kids.
Continuity mistake: When Doc Ock attacks Peter in a cafe with MJ, he throws Peter at the wall. When Peter stands up of the wall and walks outside you can see everyone panicking and screaming. In the shot when Peter takes off his glasses and the glasses hit the floor, you can see in the background that everything is quiet and no-one is panicking, as if nothing happened. (01:32:50)
Continuity mistake: When Peter first sees the burning building, there is a far away shot and you see the guy with dreadlocks run to a woman. Then it cuts back to Peter as he tries to become Spiderman then remembers he can't. Next shot has the same shot, only this time it's a close up of the man with dreadlocks running to the woman.
Continuity mistake: After the bank scene where Spidey saves aunt May from Doc Ock, while they are on the street the sun changes between shots.
Continuity mistake: People behind the pizza guy who stops Peter's motorbike disappear/reappear between shots.
Continuity mistake: During the cafe scene, the spoon under the saucer disappears in the close-up.
Continuity mistake: When Jameson is brought the suit, the position of his secretary's right arm is inconsistent between the front and back angles.
Continuity mistake: When Peter and Mary are talking in the cafe, the same cyclist with a purple shirt and a yellow bag passes by three times repeating all the previous movements.
Continuity mistake: When Mary Jane and her boyfriend are talking at home, the cushion behind wrinkles itself between shots.
Continuity mistake: When Dr. Ock climbs a building, a girl stands by a Venice poster panicking. She then walks backwards to the left, but when the angle changes she is now several meters to the right, the opposite direction she walked to.
Answer: Unless there is is a deleted scene to shed light on the issue, then it's not really addressed in the movie. It's possible that Doc Ock and Harry had a second meeting that took place off-screen in which Ock revealed to Harry where his hideout was, but as there's nothing really to go on, it's anyone's guess and it's reasonable to consider it a plot hole.
Phaneron ★