Continuity mistake: In the scene where Gwen sees Peter in the restaurant she places one hand on his shoulder. The camera cuts to Gwen's face and she has both hands clasped together in the shot. The shot cuts back out and her hand is instantly down on Peter's shoulder. It cuts back to Gwen one more time and both of her hands are back up near her face.
Continuity mistake: In the scene where Peter asks Harry to help rescue M. J. (from Venom and Sandman), a sitting chair appears to the left of the painting of Harry's father in the last shot of Harry. There was no chair in the other shots of this scene. The sitting chair was by that painting for all of the movie except those few shots.
Continuity mistake: At the end of the movie MJ is holding onto Harry's hand with both of her hands. There's a quick cut back to a view from farther away. Peter and Harry are in the same positions, but one of MJ's hands has instantly moved down around Harry's chest.
Continuity mistake: When Mary Jane halts the cab, there's a couple walking behind her, who disappear in the close-up of her opening the door.
Continuity mistake: Down in the sewer, the wad of dollar bills moves away from the puddle between the close and wide angles.
Continuity mistake: Before Harry throws the bomb at Evil Peter, two bombs can be seen together next to the place where he is lying. Half a second later, when Harry picks up one of them, the grenades are apart from each other.
Continuity mistake: The first time Peter is out and about as black Spidey, Eddie Brock runs up behind him and raises his camera. We then cut instantly to a shot of just Eddie, and he no longer has his camera raised, with no time to move it between shots.
Continuity mistake: Eddie exits the cab and runs towards Black Spidey. From a low shot Eddie's legs slow down and walk really slowly towards him. Then from a close-up of him he is seen running again and then stopping.
Continuity mistake: When Peter lands on the cab, MJ has her fringe all messed up and says "Peter, we'll both die". angle on Spidey, and when back to MJ she's perfectly combed and neat looking.
Continuity mistake: When Sandman leaves his ex wife and daughter, the daughter's position swaps from standing in the middle of a corridor to laying very close to a wall.
Continuity mistake: At the end of the final battle involving all 4 superheroes, Sandman destroys the building's iron structure with a blast of his hand, but in further shots it appears undamaged.
Continuity mistake: When Peter first goes to see Aunt May and tells her he's going to ask her to marry him, Aunt May in the first shot goes to hug Peter on his left shoulder, it cuts away and in the following shot she has hugged Peter on his right shoulder so that the camera can see Peter's face.
Continuity mistake: When the steel beam is sweeping the floor underneath the destroyed office, the model in pink disappears from the wide angle.
Continuity mistake: When the office floor collapses, Gwen and a girl in green are struggling not to fall down. In a close-up, one second later, the girl is replaced by a chair. She can be seen several meters away, next to a guy who magically appeared on scene.
Continuity mistake: During the "Keys to the City" ceremony, when people are chanting for Gwen Stacy to kiss Spider-Man, some of the same extras can be seen standing among different people in the crowd, in successive shots.
Continuity mistake: When the steel beam destroys the office, it breaks a window and a pillar. From the outside, the pillar is intact.
Continuity mistake: In the bell tower, when the slimy thing falls on Eddie, he covers himself with both hands. In the close-up his hands are down and raises just one of them.
Continuity mistake: When Peter is thrown against a brick wall, he produces a big hole around his left shoulder. In the close-up the hole is smaller.
Continuity mistake: Peter opens his shirt wide to see his evil Spidey suit underneath. When the angle changes, a frame later to a close-up of his neck and face, his shirt is closed.
Continuity mistake: Before the cop climbs on the truck, he shields himself on the truck's cabin and you can easily notice the tarp is perfectly tied by a dozen strings. When he climbs up, all the knots magically untie and he manages to pull the tarp away. His buddy couldn't have done it because he always appears with the gun in his hand, covering him.
Chosen answer: Answered in the comics: Peter's Spider-Sense tells him if someone is looking when he's about to enter/exit the apartment as Spider-Man.
Captain Defenestrator