Deliberate mistake: When Spider-Man attempts to rescue Aunt May from Doc Ock, May's umbrella handle latches onto the building's angel sculpture, so the angel is to her right. After Stan Lee's cameo, as May shouts, "Help me!" the watch is on May's right wrist instead of her usual left. When Spider-Man shouts, "I'm coming," next shot of Aunt May shows her hanging from the opposite side of the angel's body. Then Spider-Man shouts, "Hang on," and in the next close-up of Aunt May her watch is on her right wrist again. (00:50:40)
Other mistake: During the hospital scene where the robotic arms kill all the operating room staff, we see 4 different camera angles on the last doctor to be killed. All the arms have cameras in them, and show his face screaming at 4 different angles. Yet it should only be 3 as one arm has its claw wrapped around his neck. And it doesn't release from him, as it can be seen still wrapped around his neck by the other 3 cameras in each claw.
Continuity mistake: When Spidey faints after stopping the train he is carried away by the passengers. One of them raises her right arm to help. A shot later her arm is lowered, and she is raising it again. (01:36:00)
Continuity mistake: Right before Spidey stops the train there's a lot of people inside next to him. Then a wide shot later they've vanished only to reappear a shot later.
Continuity mistake: Spidey throws a huge iron minute hand at Ock which destroys an enormous chunk of concrete and makes loads of debris fall downward. However, a shot later there's a view of the street and the train track and not only is the debris gone from the road but the traffic and people act as if nothing had happened.
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.
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.
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: 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.
Answer: While it's never mentioned in the film, the most likely explanation is that Harry, as a rich kid, grew tired of "slumming it" and decided to move back into his mansion.
Harry and Peter's relationship quickly turned sour after Peter refused to discuss Spider-Man as Harry felt Peter knew more than he let on. Peter is Spider-Man's "personal photographer," and Harry only wants to avenge the death of his father. It's not unlikely to assume Harry left to live alone because he was angry Peter wouldn't help him find Spider-Man.