Continuity mistake: When we see MJ and her fiancee in her room close to the end, MJ says to him "Lean your head back for me." Her hand is not in his hand in one shot, but is in another. (01:23:40)
Continuity mistake: Just after the car goes through the cafe window and almost hits MJ and Peter, they both get up and most of MJ's hair is blown back over her shoulders. However, in the following shots, there is now a lot more at the front of her shoulders, than in previous shots. Throughout the movie, her hair changes position in consecutive shots. (01:27:15)
Continuity mistake: Near the end of the film when Peter takes his costume back from inside the Bugle, Peter's boss at the Bugle takes down the note left in a web, in one shot his fingers are half way up the note, in the following shot there right on the edge. (01:29:50)
Continuity mistake: When Spider-Man takes back his suit from Jameson's office, Jameson looks up at the skyline, and there are no steel or metal bars running over the skyline, yet when the camera zooms out with Jameson yelling "I want Spider-Man", metal bars have appeared over the skyline that were not there in the previous shot. (01:29:55)
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 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 Spider-Man is on the train with Doc Ock, Spider-Man saves two people and in this shot we see a station, yet in the following shot with Doc Ock there is no station visible in the background. (01:33:00)
Continuity mistake: When Spider-Man is at the front of the train trying to stop it, the windows at the front are already smashed, yet when he spins a load of webs, the two panes at the front smash again. (01:34:35)
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: During the train scene, Spider-Man's mask had gone partially black. We also see it when Spidey puts his mask back on. Yet when Doc brings him to Harry, we don't even see a patch of darkness on his mask.
Continuity mistake: After Spider-Man recovers from the train incident, Doc Ock smashes in the other end of the train and throws the door on the floor in front of him. The camera cuts to another shot, and when it returns the door is no longer on the floor, nor is it there for any subsequent shot.
Continuity mistake: When Peter misses the class at the university, the way he holds his books/folders changes when the teacher talks to him.
Continuity mistake: When Aunt May hugs Peter near her "hero" speech, she hugs him with her head to his left shoulder. The shot changes and you see that she is now on Peter's right shoulder. The shot changes back and you see her on his left shoulder again.
Continuity mistake: Regarding the scene where Doc Ock has delivered Spider-Man to Harry's mansion, when Harry pulls off Spider-Man's mask, there is a very obvious and bad splice. The "mask on" Spidey's head is in a different position and further away than the "mask off" Spidey's head.
Continuity mistake: During the final conversation between Spider-Man and Doc Ock, the rips in Spider-Man's suit keep changing. For instance, there is a tear on his right shoulder; for most of the scene, there is a single piece of black webbing left holding the rip together, but when Doc Ock grabs Spider-Man's arm, the rip now has two pieces of black webbing. Then it goes back to one.
Continuity mistake: As Peter stops the elevated train with many webs, a tear appears in his suit on the inside left arm during a closeup. Later, when his arms are still outstreched, there are many shots where you can see that the tear has disappeared; for example, a few shots later when he is still trying to stop the train; when the passengers are lifting him over their heads into the train; and many others.
Continuity mistake: In the scene with Peter's "I'm back!" jump, It shows a shot from above and you can see his solid outlined shadow in front of him. However, in the very next shot it shows you a close up of Peter walking, and there is no longer a shadow there.
Continuity mistake: When Peter visits the doctor, look closely at the skeleton behind him. In the first shot, you can see two spots of light reflected on its skull; in subsequent shots, there is only one spot of light.
Continuity mistake: When Doc Ock carried MJ up the side of the building after he kidnapped her, one of the D'Agostino banners was ripped out of the building and fell. But when Peter came out of the deli and looked across the street, the banner was back on the building and the building wall showed no sign of damage from Doc Ock's tentacles.
Continuity mistake: There are two close-ups of Peter's head when he is lying on the floor of the train: one of the shots has a black shoe with white laces very near his head, the other a blue, white, and black shoe, also right next to his head. In the wider overhead shots of Peter, no one standing around him is wearing shoes like that, nor are they standing close enough for their feet to be in the close-up shot in the first place.
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 ★