Continuity mistake: As Peter is walking along the top of the building, about to do his "I'm back" jump, he is about three quarters of the way past a skylight on the roof. Then the shot changes, and he is just walking up to it.
Continuity mistake: When Peter is on the rooftop, just before he does his "I'm back" line, he begins to run. He runs quite some distance before it goes to slow motion, yet a few shots later during the slow motion, he is back to where he started running. (01:22:05)
Continuity mistake: As Ock climbs the building with Aunt May, a girl is on the phone and feels the trembles. She hangs up the phone and gets up to look out the window. At the desk in front of her, there is an employee helping a customer. As the first girl goes to the window, the customer gets up to leave. The tentacle crashes through the side of the building, the camera pans out and the employee helping the customer is away from her desk, the chair is pushed in and the phone is off the receiver.
Continuity mistake: When Peter is being fired from his pizza place job, there is a clock behind him. While the clock is on Peter the second hand is near the 4. The shot then changes to the boss and then goes back to Peter about 10 seconds later, so the second hand should be on the 6 or the 7, but it is up at the 2.
Continuity mistake: On the way to the play when Spider-Man is chasing the criminals in the car, the passenger is using a shotgun which switches to an automatic weapon which then switches back to a shotgun in a matter of seconds. There is no time for him to switch the guns that fast in the scene.
Continuity mistake: When the car flies past Peter's head, we have a full view of the tire rim which means we are looking at the side of the car. But this view is only possible if the car were thrown in head-first or tail-first, which wasn't the case.
Continuity mistake: At the end of the "I've changed" conversation with Mary Jane, the taxi is right next to her as she turns towards it (you can see its roof next to her face), yet in the very next shot she has to cross the street to get to it.
Continuity mistake: When about to deliver the pizzas, Peter's hair swaps from messy to brushed.
Continuity mistake: When Harry is held upside-down by Doc Ock, his tie is tacked to his shirt partway down (so it doesn't fly in his face). A couple seconds later, on the balcony, Harry's tie is not tacked.
Continuity mistake: While in the bank trying to get a loan, there is a desk with two chairs behind Peter and Aunt May. As Doc Ock throws the vault door in their direction and Peter kicks the two of them out of danger, there are no chairs at the desk behind them.
Continuity mistake: In the scene where Aunt May is outside her house, packing things into boxes, we see a close-up of her holding what appears to be a large black leather shoe at upper chest level. The next shot is a wide shot of the yard, and now she's holding it in a different position near waist level.
Continuity mistake: The spiderweb that Harry brushes aside is missing from two previous shots: from inside the secret lair looking out at Harry, and from the reverse shot looking into the lair.
Continuity mistake: In the final conversation between Peter and Mary Jane at his doorway, the lighting on his face switches in every shot.
Continuity mistake: When John Jameson and Mary Jane are walking down the stairs during John's celebration party, there are two people halfway down the staircase standing by themselves. When it does the closeup of John and Mary Jane, there are four people now standing in that spot.
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.
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.
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: 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.
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 ★