5. Peter Parker's career choice
There's no denying it: Peter Parker is a genius. He's considered one of the smartest people in the Marvel Universe, coming only behind the likes of Reed Richards and Tony Stark. Many different parties have tried to replicate his web-fluid formula but they all have failed, indicating how smart Peter really is.
With that in mind, it's insanely perplexing to know he works in the Daily Bugle taking pictures of Spider-Man instead of, you know, somewhere else where his wits are taken advantage of. He could definitely land a better-paying job and avoid many problems like being evicted from this building or watching his aunt struggle with payments.
To be fair, many recent adaptations of the character have realized this is an issue and tried to rectify it. In Marvel's Spider-Man for PS4, Peter worked for Otto Octavius trying to create an advanced prosthetic limb, which would eventually backfire by giving birth to Doctor Octopus' metal arms. Besides, Peter is also the CEO of Parker Industries in Earth-616, a research and technology company.
Still, that doesn't take away from the fact that whenever you talk about Peter Parker, people often picture him as a broke teenager who works for the Daily Bugle. I'd understand his career choice if he at least enjoyed that job, but considering J. Jonah Jameson treats him poorly and publicly shames Spider-Man every chance he gets, I can't imagine that being a good working environment at all.
... And don't even get us started on how it doesn't make sense for the spider-sense to be so inconsistent, because we could be here all day long.