Continuity mistake: After Doc Ock throws the car through the side of the deli, it shows Peter and MJ from outside the building and there's a table with a chair at the base of the hole right up next to the nonexistent wall. For the rest of the scene, the table and chair are not there.
Other mistake: When Peter Parker is walking down the streets of NYC on his first day as a "normal, powerless human" It is clear that the people in the background are not extras. You can see several people watching him during the shooting of the scenes.
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: 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)
Revealing mistake: In the scene where Spider-Man is pushed inside the train by Dr. Octopus and grabs the bar then leaps to the next: The passengers are all looking where they've been told Spider-Man is supposed to be, but none of them are actually looking at him, revealing that he is a CGI image and not an actor.
Factual error: When Spider-Man is fighting with Doc Ock and Doc Ock throws Spider-Man through the overhead pedestrian bridge, Doc Ock throws Spider-man in the direction of travel of the train, and when passing through the bridge, Spider-Man doesn't touch anything. When Spider-Man comes out the other side, he is "behind" Doc Ock (in terms of the direction of train travel). This implies that Spider-Man has slowed down in the air - fair enough due to wind resistance - and so is traveling slower. However, Spider-Man then hits Doc Ock from behind, meaning he's now sped himself up in mid air. He doesn't use any webs.
Other mistake: Sure Spider-Man has super human powers, but his costume doesn't (as we see as it rips and tears quite a lot through the movie) so how come the back of it is still intact and not even dirty after being dragged over the street by a train that's going at high speed?
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: 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: 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)
Revealing mistake: In the scene right after Peter and MJ swing off and they are on the web, Peter is crawling toward MJ. You can see on his right thigh that where there is a tear mark that his skin isn't showing through, but instead there is a piece of flesh toned material. (It bends unlike the skin on the thigh would)This was probably done so the Spidey suit would still remain tight to Peter's body. (01:53:00)
Other mistake: When Spider-Man and Mary Jane are sweet-talking in the web, her hair blows around freely, whereas considering how sticky a spider web is, her hair should be sticking fast to it. Permanently. After all, the web cannot be sticky enough to hold her body, while not being sticky enough to glue her hair.
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: During the scene where Peter is on his way to the play, he stops the cop car flying through the air by catching it in a web, but the glass shards and debris which are flying along with the car are not in the web anywhere, nor do they hit the people in the path of the car.
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)
Factual error: In the scene where Peter is saving the children from the burning building, there is no smoke from the fire, when there should be black smoke billowing out the windows. He wouldn't be able to just stand up and walk through the building. But in order for the scene to play out on camera, the area is smoke free. A fire in an apartment or office building will include combusting of large amounts of plastics (computers and so on). So unless there is nothing but alcohols in the building there will be immense amounts of smoke.
Continuity mistake: As Mary Jane is reunited with John Jameson after Spider-Man lowers her down from the crane, one shot shows tears along Spider-Man's suit along the left leg while he is crouching. However, in a later shot, he stands up to swing away and the tears are now running along his right leg.
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: After Peter came out of the deli, you could see and hear people running around screaming hysterically. But when the shot showed Peter's glasses falling to the ground in slow motion, you could see people were just walking down the street leisurely.
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.
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 ★