1. So the Green Goblin mask was just lying around?
Norman Osborn just wants to make the world a better place with his gun-mounted death glider and insanity steroid serum, which is why it's such a bummer when things go to shit and he starts using them for evil. While I kind of get that, in the right hands, both the glider and the serum might have useful military applications, what the hell is the deal with the grinning yellow-eyed monster helmet Osborn uses when he starts flying around bombing people? Was Oscorp producing those too, or did Norman go crazy, design and manufacture a terrifying Halloween mask, and THEN go on a murderous rampage?
2. Peter never gets round to telling Harry about his nuts dad, even though that would fix everything
Before he dies, Norman makes Peter promise he won't tell Harry his father was the Green Goblin. Peter agrees, even though literally everybody would benefit from knowing what happened, not just to save Spider-Man's reputation but also, like, here's an idea, maybe Oscorp should be shut down for the sake of national security. Also do you really need to be TOLD that the crazy guy in an Oscorp suit on an Oscorp glider throwing Oscorp bombs was the head of the company, who happened to die at the exact same moment the Green Goblin disappeared forever?
Anyway, Peter keeps the secret for way longer than he should, considering his best friend has sworn vengeance against him for no good reason, and seems to be going kind of crazy himself. Just tell him, dude.
3. Doc Ock is terrible at robbing banks
Doctor Octopus is a genius nuclear scientist who very nearly figured out unlimited renewable energy. Doc Ock, the genius, decides to rob a bank with his indestructible robot arms in order to fund another attempt at unlimited renewable energy, which makes sense. When he robs the bank, Doc Ock, who, remember, is a genius, steals nothing but sacks of Sacagawea dollars. Those bags probably hold, like, $500 max, right? Even with his extra arms, that means he was planning on stealing around $3,000 to invent from scratch the most important device in history
4. Wait so Doc Ock's arms control his thoughts? That's dumb.
There's this whole plot in Spider-Man 2 about how Doc Ock's arms are kind of sentient and can control his thoughts, even though it's never really established how that's possible. It just kind of confuses the whole idea of him being a villain. Is he just a nice guy being held hostage by his intelligent robot arms? There's no reason for this to have been a thing at all. His life's work was destroyed and his wife was killed 2 hours ago. You can definitely be evil after that. It's fine.
5. People always cheer and clap after Spider-Man does something good, even though something terrible's just happened
Get it together, guys! Just because Spider-Man saved, like, ONLY his girlfriend, doesn't un-blow up that entire building. Things are still really scary and dangerous and very much on fire. Run. If I saw that kind of large-scale destruction I would throw up and faint instantly, regardless of how many hot redheads survived.