Continuity mistake: When Spidey runs out of web and plummets on some metal tubes, he lands with both arms up. A frame later one is up and another by his side.
Continuity mistake: When aunt May places flowers by her husband's grave a green plant suddenly appears on the left side, between shots.
Continuity mistake: In the bank, when Dr. Ock is throwing bags with coins at Spidey, a bunch of folders on the right appear / disappear randomly depending on the shot.
Continuity mistake: During the cafe scene, Mary Jane's hair on her left side is stuck under her hat. When the angle changes, it's not.
Continuity mistake: When Dr. Ock punches the yellow cab, the cabs on the left disappear, only to reappear seconds later.
Continuity mistake: Dr. Ock points at the chip with his finger on his nape, but when the angle changes the finger is away and is approaching the nape again.
Continuity mistake: Dr. Ock flies through the bank window and crashes against a cab, next to a metal cabinet. The cabinet changes positions between shots.
Continuity mistake: When Dr. Ock is thrown out of the bank he breaks a shop window, leaving no glass bits standing out of the frame. A second later there are glass part all around the window.
Continuity mistake: Box on the table moves between shots, when Peter and Harry talk during the birthday party.
Continuity mistake: Spider-Man falls on a puddle and looks at the wall in front. There's a window to his right, barely a metre from the floor, and an emergency staircase on the left. When he starts climbing, the staircase disappears and the window is now 10 metres above the ground, on the left side.
Continuity mistake: When Peter parks the car by the theatre door, two women walk past the cop twice.
Continuity mistake: When Doc. Ock exits the hospital, the cab in front passes by the same zebra crossing twice.
Continuity mistake: After Spider-Man stops the train and faints, four hands comfort him. A frame later they've changed positions.
Continuity mistake: Before Spider-Man saves the kids from being run over, they're running and are inches away from the road. Five seconds later, after several flying scenes, they've moved 5 metres behind and are running towards the road again.
Continuity mistake: When Peter crosses the campus, its avenue is almost empty, but in the close-up it's filled with people.
Continuity mistake: When Peter stops his bike by the pizza man, a guy entering the store on the left disappears.
Continuity mistake: When Peter bounces into Professor Connors, the passers-by behind are not continuous between shots.
Continuity mistake: The wrinkles on the sticker on Peter's helmet change between shots.
Continuity mistake: Before Spider-Man saves the children, the black truck runs by the same yellow cab twice.
Continuity mistake: After Spider-Man scolds the kids for playing on the street, the boy's hair swaps from messy to brushed. When Spider-Man leaves, it changes back to messy.
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 ★