(at around 1h 19 mins) When Peter Parker saves the child from the burning building, she is old enough to stand and help him up. However, when he hands the child to the parents after exiting the building, the fake bundle he hands them is the size of the infant.
(at around 52 mins) After fighting outside of the bank, Doc Ock is carrying no money bags. There are many shots showing all his free hands and even when they leave the bank initially there is nothing in his hands. Then when we see Doc Ock leaving there are two money bags in his tentacle.
(at around 1h 30 mins) The car thrown by Dr. Ock comes through the window sideways, yet when it flies over Peter and Mary Jane, you can see by the position of the wheel that it's flying straight. It lands sideways again.
(at around 48 mins) When Doc Ock robs the bank, his mechanical arms appear from nowhere.
(at around 1h 30 mins) The wheels on the car Doc Ock throws through the cafe window are spinning as it flies over Peter and Mary Jane. But when it lands moments later, the wheels are stationary.
Tritium is actually a gas isotope (Hydrogen - 3) and as such would not be a solid at room temperature.
(at around 48 mins) When Doctor Octopus exits the hospital, two of his mechanical arms pick up and throw a taxi, while the other two brace themselves on the street. But when he rips open the bank vault, he uses all four arms. This would be impossible unless his real legs and back had the strength to lift the vault door.
(at around 1h 26 mins) When Peter tries his "I'm back" jump, he is moving in a parabolic curve until his jump fails and he drops straight down into the alley. Physics states that he would have continued on his parabola, causing him to hit the wall at some point.
During the burning building scene Peter tries to open a closed door with the only trouble being that he can't open it. In reality, superhero or not, the doorknob would've burned his hand due to the incredible heat.
(at around 1h 35 mins) When Octavius and Spider-Man are fighting on the train, Octavius throws him forward through a bridge and Spider-Man subsequently lands on top of him. This is physically impossible unless the train sped up fast enough to match Peter's speed in that time frame which is very unlikely, or Peter was somehow able to slow himself down whilst airborne, which also seems unlikely.
In the train fight sequence, the train says Bay Ridge in the destination window on the front of the train. On real subway cars, there are no destination signs on the cab ends of the cars: only a letter or number rollsign or LED display is present. The only destination signs in the trains are on the sides of the cars. Historically, however, there has been New York City Subway rolling stock that has been equipped with end destination signs (like the Redbird trains used on the IRT until 2003, and the R32 and R38 cars prior to being retrofitted with flipdot signs in the 1990s). Despite this, no rolling stock has been built for the subway with blinker doors. All stock has been constructed with sliding doors. However, this is a fictional route created for the movie (see Trivia), and it might not necessarily be tied in with the real subway system.
(at around 48 mins) In the bank, when Doc Ock throws the vault door at Peter and Aunt May and they slide to either side of it, you can see the cables under Peter's chair used to pull it. (Corrected on the DVD.)
(at around 1h 40 mins) When Spider-man is carried back into the train one of the hand rails wobble, indicating that it is made of rubber.
(at around 1h 55 mins) As Mary Jane runs from her church wedding her hair is parted on the left. When she arrives at Peters her hair is parted on the right (mirrored image).
(at around 1h 10 mins) After the cemetery scene and before Peter confesses about Uncle Ben, there is an establishing shot of Aunt May's house. The way her yellow car is parked in the driveway leaves no way for the doors to open. The space between her house and MJ's parents' house is too narrow. Obviously the car was rolled in to obtain the shot.
(at around 1h 18 mins) During the fire scene, Peter falls through the floor and the girl helps pull him up. As she rises to her feet doing so, kneepads can clearly be made out beneath her pajamas.
After Spiderman saves M.J. from doc Octavius and lowers her from the crane so she can run to her fiance they show Spiderman shooting a web up in the sky to swing away on. The only problem is that in all the shots of doc Oct's lab/lair there aren't any tall buildings by it. It is on a dock by the river. The crane Spiderman is on is the tallest structure in the area so there wouldn't have been anything for the web to catch on to so that he could swing away from.
(at around 34 mins) When Octavius introduces his four arms, and as he turns to have the device attached to his back he says, "They are impervious to heat and magnetism." As he turns his lips are not moving but we hear him speaking.
(at around 10 mins) When we first see Aunt May in the movie, she's speaking while kissing Peter but her lips are not moving.
(at around 50 mins) When Aunt May is yelling during the first fight sequence with Doc. Ock, her mouth doesn't match.
(at around 56 mins) During the party at the planetarium, the saxophone soloist's fingers are not going along with the music that can be heard.
(at around 1h 22 mins) When Peter is talking with Aunt May while she's loading boxes out of the house, you can see the shape and bulge of his microphone and wire under his shirt.
(at around 25 mins) When the police car rolls during the chase, the driver is wearing a stunt helmet.
(at around 25 mins) On the way to the theater Peter intercepts a police officer chasing a couple of criminals. At the end of that scene one of the police cars has a tremendous wreck that swings the car sideways. There is a clear shot of the driver with a black helmet on.
(at around 2h) At the very last scene of Mary Jane looking over the city in Peter's apartment, there is a reflection in the window where the camera lens and cameraman are partially visible.
(at around 32 mins) Boom mic reflected on upper part of phone when Peter puts a 50 cent coin in.
(at around 1h 10 mins) In Spider-Man (2002), Uncle Ben's grave was surrounded by other graves, but in this film there are no others in sight.
There are no elevated trains in Manhattan running near skyscrapers or between high-rise buildings. The longer shots of the train exterior look rather like Chicago "L" lines, and in fact, the 'making of' reveals this footage was shot in Chicago.
Even though the runaway train is shown to be an 'R' service, which is headed for Bay Ridge - 95th Street (in Brooklyn), it is never shown how the fictional elevated line gets to Brooklyn so that the service could join the real life BMT Fourth Avenue Line. The line dead-ends in Manhattan, and never gets to cross the East River.
(at around 3 mins) In the first scene, at a pizzeria located at Bleecker St. & Sixth Ave., Peter's boss tells him he has to deliver a stack of pizzas to the Woolworth Building 42 blocks away. In real life, the Woolworth Building is only about 22-24 blocks away, depending on one's route.
(at around 49 mins) When Spider-man is fighting Doc Ock for the first time in the bank behind Doc Ock are the windows of the bank that he will crash into later. When you look in the windows you see a White bus with a orange line in the middle that says "Metro Bus", a Los Angeles company.
Parts of the lower side of the construction in which Doc Ock has set up his second experiment are also made of metal. This means that when the experiment fails again, the base of the building would be sucked into the tritium sphere as well. This in turn would cause the structure to collapse so that the sphere would fall into the river.
(at around 1h 40 mins) Peter asks Harry where Doctor Octopus has taken the kidnapped Mary-Jane. How would he know where his lair is?
When Peter delivers the pizzas he is 3 minutes late at 3 minutes past 2. He then arrives back at the shop where a clock reveals it is just after quarter part 2. Assuming he did not rush back to the shop this means he could have delivered the pizzas in plenty of time.
(at around 6 mins) When Peter has delivered the pizza and is untying the rope, the shadow of the boom mic is visible behind the wall.
(at around 52 mins) In the first battle scene with Doc Ock fighting Spider-Man, Spider-Man, who has strength proportionate to a spider, hits Ock plenty of times, not only with his fists, webs, and feet, but with a desk and a window, too. All of these times Ock barely flinches with the blows. And yet, at the end of this scene, the elderly Aunt May clubs Ock over the head with an umbrella hard enough not only to make him back off but to break his sun glasses which were previously unscratched.
(at around 3 mins) When Peter is in the Pizzeria, his boss tells him to deliver the "deep dish pizzas". Later on when the pizzas are on the balcony, and the box is opened, they are revealed to be thin crust.
(at around 1h 20 mins) Ursula asks Peter if he wants a piece of chocolate cake; however, in the next shot you see Peter finishing off a white sponge cake.
(at around 19 mins) When Harry talks about Dr. Octavius' chances at winning the Nobel Peace Prize, he walks out of the scene saying, "See you in Sweden!" Although the Nobel is named after a Swedish man, the Nobel Peace Prize ceremony is held in Oslo, Norway. An easy mistake to make.
(at around 7 mins) The sticker for the pizza parlor on Peter Parker's helmet says "Bleeker Street". The street in lower Manhattan is actually Bleecker.