Continuity mistake: At the very beginning when Peter walks into the pizza place with his boss, a policeman walks out, In the following shot, the policeman has vanished. (00:03:30)
Continuity mistake: On his last pizza delivery before he gets fired, when it first cuts to the receptionist and the room that she is in, the clock is very high up in this shot, above the receptionist's head, then in the following shot when the receptionist is looking in Peter's direction, the clock is much lower. (00:05:35)
Continuity mistake: At the beginning of the film when we see Peter in Jameson's office, the black guy says, "Five minutes to deadline Jonah." Jameson raises his hand to him, but in the following shot it's a lot lower. Also, when he's talking about a food poisoning scare, he raises his hand high up to the right, yet in the following shot, it's far to the left of him. (00:07:45)
Continuity mistake: At the beginning of the film, Peter bumps into Dr Connors. Peter has his bag on his left shoulder but in the previous shot you don't see him put it on his left shoulder. (00:08:45)
Audio problem: When Aunt May gives Peter his birthday money, before she says, "Can you believe that it's two years next month since he was taken?", we see her from the side, and the motion of her jaw shows that her lips are moving before she speaks. When she says, "Were I to face the one responsible.", there's another shot of her from the side, and as she continues, ".for what happened", her jaw doesn't move at all. In the same shot, when she says, "Oh, I don't know what I'd do", once again the motion of her jaw show that her lips are moving before she speaks. (00:13:20)
Continuity mistake: In the scene where Peter is riding his scooter to Mary Jane's play, after the music fades out you see a black convertible being chased by several police cars. The black convertible is rammed forcibly, and you see many hideous dents on the side of the car. Thirty seconds later, after Peter is done talking to the kids, we see the same car from the same side it got rammed into, but the hideous dents have vanished. (00:24:25)
Continuity mistake: When Dr. Octopus is robbing the bank, NYPD squad car 4619 arrives on the scene. However, squad car 4619 was badly damaged during the pizza delivery car chase earlier in the movie - an awfully quick fix. (00:24:55 - 00:49:45)
Continuity mistake: Peter has a small horseshoe-shaped scar on his right cheek. In Dr. Octopus's lab, as Octopus is destroying the fusion reactor, they share a meaningful look and the scar has switched cheeks. (00:26:15 - 01:46:15)
Continuity mistake: In the elevator scene when Peter/Spider-man first loses his powers, we see a man standing outside the elevator holding a dog on a leash. However, after Spider-man delivers the line about the costume riding up on the crotch, we see the man use both hands to adjust his jacket, and the leash is nowhere to be found, nor is their any indication that the dog is on the elevator. (00:29:30 - 00:30:35)
Continuity mistake: When the people are watching Doc Ock with his experiment, Rosie is standing at the bottom of the stairs. When Doc Ock passes her his coat, she is then seen in the background standing next to a large TV screen. (00:32:35)
Continuity mistake: When Doc Ock robs the bank, Peter pushes Aunt May away, but in one shot he turns his chair to push away, yet in the following shot the chair is facing a different direction. (00:46:10)
Continuity mistake: As you are listening to the bank guard tell Doctor Octopus, "Put your arms up! All of them!", look at the money cart inside the vault. It goes from just a few items on it at first, to having a multitude of items on it, as well as around it, in later shots of the scene. (00:48:15 - 00:49:05)
Continuity mistake: Just after the bank robbery, Spider-Man and Doc Ock are on the side of the building. Doc Ock says "oops, butterfingers." Spider-Man shoots a web to catch Aunt May. In this shot, Spider-Man is on one knee with the other one resting on the wall, yet in the following shot he is standing up and leaning back to pull Aunt May up. (00:48:25)
Continuity mistake: Just after the bank robbery, Doc Ock and Spider-Man are fighting on the side of the building. When some rocks fall down, there is a man (that looks like Stan Lee) pulling a girl away from falling debris. There is a red car to the right of the screen and a yellow taxi to the left, yet in the following shot from a different angle, there are a few more people in front of the red car, and no dust on the ground where the rocks hit the floor. (00:48:35)
Continuity mistake: Close to the middle of the film when Peter is in the big room where MJ announces her engagement, when Peter is finished talking with Harry at the bar he gets pulled away by Jameson, Harry then turns around and drinks, yet when it cuts to a shot of Peter and Jameson walking away, look in the background and Harry is still looking at Peter walking away. (00:51:45)
Continuity mistake: When Aunt May is falling off the building, her purse is on her right arm. The next shot shows the purse on her left arm. (00:52:05)
Continuity mistake: When Peter starts to lose his powers, and tries to climb up the side of the building, in several shots, he is by a window, and he slips opposite the window, yet in the following shot he is a lot further above the window. His distance and position from the window changes in subsequent shots. (00:56:30)
Continuity mistake: When the garbage man enters Jameson's office, Jameson is holding a phone to his chest, yet in the following shot he is not holding the phone, and we didn't see him put it down in the previous shot. (01:05:40)
Continuity mistake: When the garbage man is in Jameson's office, and Jameson is holding the Spider-Man suit, he is holding it almost at arms length to his right, yet in the following shot, it's a lot closer to his body. (01:05:50)
Continuity mistake: Near the end of the film when we see Peter looking out of his window from his apartment, the girl from across the hall offers chocolate cake. When they are done eating, Peter is holding the fork with his thumb and in the following shot he is not. The fork has moved across the plate a little between shots. (01:17:30)
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 ★