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: After knowing that Mary Jane is to be married, Spider-Man falls on a puddle, but no water drips from his suit. Seconds later, he falls again and now water does drip.
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.
Continuity mistake: When Peter stops his motorbike by a grocery store, a group of children suddenly appear out of nowhere.
Continuity mistake: When Octopus's house is about to fall on Mary Jane, the box to her left swaps to being on the right side in the front angles.
Continuity mistake: Mary Jane runs in her wedding dress by a fountain in an empty park. A frame later it's packed with people.
Continuity mistake: When Peter and MJ are in the cafe, before Doc Ock attacks, the same sequence of cars and pedestrians outside the window goes by several times. Pay particular attention when the taxi goes by.
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 ★