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.
Visible crew/equipment: After he watches Mary Jane exiting from the theatre with her boyfriend, Peter is running in the alley to put on the costume. On the wet ground you can see the traces of the tires belonging to the camera car used to shoot the scene.
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.
Revealing mistake: During the final battle, when Spidey tells Doc Ock "we have to give up the thing we want the most... even our dreams", watch the tentacle behind Doc Ock's head. Right after Spidey says "even our dreams", the three "claws" on the tentacle close, and you can see the tip of the bottom "claw" pass through the tip of one of the other claws, revealing a blunder in the rendering of the digital effect. (This is visible in the DVD release of the theatrical cut of the film. It was corrected in the "2.1" edition, and may have been corrected in the Blu-Ray release, but it's still plainly visible on the original DVD release).
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: The chip on Dr. Ock's nape is 10 centimeters away from his hair. In the close-up it's right next to the hair.
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.
Continuity mistake: Dr. Ock punches a yellow cab which flips over and is about to land on its side, inches away from the floor. When the angle changes, the cab is now a couple meters above from the floor, with a cab underneath, plus it's falling on it's 4 wheels.
Continuity mistake: Spidey falls on a puddle and takes off his mask, his hair completely messy and wet. A frame later, when he is about to climb a wall, it's neat and brushed.
Continuity mistake: When Dr. Ock kidnaps Mary Jane and walks by a bluish car with a girl laying on the hood, panicking, a boom mic is reflected on the windshield.
Continuity mistake: During the bank robbery, Aunt May cries "Don't leave me!" and the distance between her head and the bank worker's swaps from close to far between one frame and the next.
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 ★