Other mistake: At the end, when Peter saves Mary Jane from the collapsing structure, he jumps up in the air and swings her to safety. However if you look at the web he is holding onto it is hanging down vertically. What did he attach the web to that was directly above him, the sky? Every bit of the structure around him was/had collapsed and the only thing remotely close to swing from was the cranes. Yet we see that was quite a distance away, so Peter would have had to shoot the web away from himself not above him. (01:47:50)
Other mistake: When Spider-Man shoots a single web out of each arm to stop the train, in the shots of his reactions, you can see that he is holding many webs in each hand. Then when he shoots multiple webs to try and stop the train, he has the same amount of different webs as before. Obviously they didn't have footage of him just holding a single web, and used shots from later in the sequence.
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.
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?
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.
Other mistake: This mistake can be seen in Swedish theaters: right in the end where Peter Parker says "Thank you, Mary Jane Watson" the Swedish subtitles say "Wilson" instead of "Watson".
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