Continuity mistake: When Peter is visiting Harry in the hospital you can see behind Peter an admissions desk with a computer, files etc., yet when Peter and MJ leave Harry at the request of the nurse, the admissions desk has vanished and has now turned into just a plain long corridor with rooms to other patients.
Continuity mistake: When the Captain arrives at the crane scene, he parks on the right side of the street, next to the curb. When he looks at the chaos, the POV and his position show him on the left curb.
Continuity mistake: When Edward enters JK's office the secretary stands up and picks up the phone. In the next angle the phone is gone.
Continuity mistake: In JK's office, the first three bottles of pills are equidistant from each other. From the back, two of them are very close together.
Continuity mistake: In the bell tower, Eddie throws his jacket to the right, but it appears on the left side a second later.
Continuity mistake: At the very beginning of the film when we first see Peter, 4 kids stand beside him and watch Spider-man on the big screen. Watch closely when they walk away, the little girl walks off first followed by the 3 boys, yet in the following shot the girl is at the very back with the 3 boys leading the way.
Continuity mistake: When Venom dies, from the front shot Peter takes his hand away from his face. From the immediate back shot he still has it placed there.
Continuity mistake: During the Peter/Harry fight at the beginning of the film, when Peter retrieves the ring from the air and then falls onto a rooftop, if you watch closely the large air vent moves from being from Peter's right out of shot, and when the shot changes to him starting to run, the air vent is now much further behind him.
Continuity mistake: In the scene where Spider-Man is receiving the key to the city just after he kisses Gwen, we see MJ walk away and Harry standing next to her asking if she's okay, in this shot we can see her handbag has slid down her arm and is resting on her forearm, yet when the sandstorm breezes through, the angle cuts to the back of MJ and Harry and in this shot we can see the handbag is still on her shoulder.
Continuity mistake: When Peter is blinded by the metal pen in class, he covers his eye and forehead. A frame later, the new angle shows his hand away from his face, covering part of the eye and cheek.
Continuity mistake: In the scene where we first see Jameson sitting at his desk watching the other guy explaining something on the whiteboard, Jameson's cigar keeps constantly changing between shots from being in his mouth, to being in his fingers and being in the ashtray, all this happens when Jameson's secretary first interrupts him and tells him to watch the anger.
Continuity mistake: When JK is receiving a marketing lesson in his office, the amount of water in his glass increases between shots instead of decreasing.
Continuity mistake: When Gwen is hanging on the edge of the building, the table that slides towards her swaps from being worn out and filled with scratches to new.
Continuity mistake: When Captain Stacy gets to the street where Gwen is about to fall down, a police van is parked behind him. However, in the next shot, the van is gone.
Continuity mistake: Just before Eddie gets the black suit, he enters the church and is dry, but he should be wet because of the rain outside.
Continuity mistake: Right before Sandman is turned into sand he raises his hands to protect himself. A shot later they're lowered, and he raises them again.
Continuity mistake: Before Sandman is turned into sand, the craw-like machine lifts up tons of sand but it never gets in his eyes nor sticks to his shirt.
Continuity mistake: When Peter gets Eddie out from Venom you see a lot of symbiote stays on his chest after he finally gets out from it, but in the front shot of the symbiote you see no remnants on his chest.
Continuity mistake: When Peter is talking on the phone with Dr. Connors in his apartment, the hand that's holding the phone switches between shots. In the first, it's his right hand, immediately after that, it's his left hand, and in the third shot it reverts back to his right hand again.
Continuity mistake: In the scene just before Mary Jane throws a hollow brick onto Eddie's head, his back is briefly shown where we can see that he is not wearing any dress under his venom suit. But later at the end when Spider-man tries to save Eddie by pulling him out, his dress comes back on 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