- Mary Jane chews Peter out for missing her play, not listening to his legitimate explanation for why he missed it in the first place, which was that, omitting his personal involvement as Spider-Man in a car chase between some thieves and the police, his scooter got ran over by said thieves during the chase. But go back to the first movie and notice how Mary Jane was used to being disappointed by others: she had a terrible relationship with her father, she broke up with Flash at their high school graduation and Harry didn't really defend her when his father accused her of only dating him for his money (we saw her reaction when Norman made that remark, making it clear how much Norman's words stung). In fact, Peter has been the only person who she could depend on. In the end, she finally realized who she was truly in love with, and it was Peter. But Peter couldn't be with her because he's Spider-Man. So when Aunt May, Harry and even her father showed up to see the play and Peter didn't, it's no wonder she gave him the cold shoulder afterwards.
- The fact that Mary Jane is in love with Peter also explains a lot of her behavior around John and why she abandons him at the altar. In that one scene with John at the party, she wants to see if she feels the same thing she felt when she kissed Spider-Man. She feels nothing. Then, at the coffee shop, it's clear she wants to try it on Peter, at least until Doc Ock interrupts the moment by throwing a car through the window and then showing up to abduct Mary Jane. When she sees that Peter and Spider-Man are the same person, she's just stunned. She came to realize that all those times Peter was unavailable, he was out there saving people, and knew now for why they couldn't connect before. It's also important because nobody else really saw Mary Jane as a person throughout the trilogy. Nobody saw her and wanted to be with her because they didn't care about her besides Peter. And as much as Peter declined to be with her for her safety (given Norman kidnapped her as bait after figuring out his secret in the first film), she pushed that aside because she knows now that Peter has genuine love for her and she's willing to put up with it now and risk her life for it. Because that's what she wants to do with her life.
- The "cake scene" is often pegged as a pointless Big-Lipped Alligator Moment. Basically, Ursula invites Peter over for a slice of cake, and he sits there eating in awkward silence for a minute, enjoying the cake but not having anything to say to her. The scene was emphasizing that despite the Character Development over the past film-and-a-half, deep down, Peter is still a socially awkward geek who can't relate to people. This casts new light on his relationship with Mary Jane — whom he can talk to.
- When Harry asked Peter why he killed his father, Peter simply doesn't answer, saying there are more important things going on (what with Ock holding Mary Jane hostage). Many have faulted Peter for not telling the truth, as it would have saved him so much trouble in the sequel. However, there are two things Peter probably realized. One, he knew that Harry's hatred for Spider-Man ran too deep to believe anything he says and he would just make things even worse at that moment. Two, he's honoring Norman's last wishes: "Peter, don't tell Harry."
- Why did Peter have to use his body to stop the train the way he did and nearly kill himself in the process, rather than use his webbing to create a cushion for the train to safely collide into? The thing is, if you know your physics, the train was moving dangerously fast on narrow tracks located above streets and sidewalks, so therefore, any way to quickly stop the train, such as using a cushion barrier, would just lead to a violent derailment. It had to slow down first before it could stop. Peter figured it out, and he also probably figured that simply creating a giant web in front of the train would probably not be enough to do the job. He needed something sturdy that would firmly keep his webbing in place and, likely thinking off the bat, put his faith in his own superhuman body to do just that.
- More Fridge Tragedy than anything else, but when Peter and Otto Octavius first meet, Otto tells Peter that intelligence is a gift, not a privilege. When Peter unmasks in front of him during the finale, he reminds him of this, Peter saying that intelligence is a gift, to which Otto responds with a nod and saying 'a privilege'. It shows just how far he's fallen, that the very lesson he taught to Peter now needs to be taught back to him