Question: How come Miles could venom strike and turn invisible on command just because of what Jeff said?
Question: Shouldn't Peter's spider sense work when he meets Dr Octopus?
Answer: She wasn't a danger to him in the moment they met. The Doc Oc from his universe was likely still the male version we all know and his senses were attuned to recognize him. At the moment they met and she started geeking out over him, she wasn't immediately trying to harm or threaten him so his senses had no reason to be triggered by a strange woman who, at that moment, seemed normal.
Question: How come that Miles and Gwen meet each other before the accident at the alchemax? Theoretically Gwen shouldn't be there since Spider-Man hasn't been "put" in the collider yet.
Answer: She explains that she arrived in his dimension a week ago: "I was blown into last week, literally". Clearly dimension-jumping can affect time too.
Question: How can Gwen pose as a student at the Academy wearing part of her costume, tights and ballet shoes, with no teacher noticing and forcing her to wear the same socks and shoes as the other girls?
Answer: Gwen is only briefly shown in school, there's nothing to suggest she wasn't given any warnings about uniform violations. If she did receive warnings, she simply didn't address them, considering she isn't even a real student. Some schools don't force students to correct uniform violations on the spot.
Question: What was Jeff talking about when he said Miles said they made a deal with the school about weeknights.
Answer: It's a boarding school, but Miles wants to return to his old school. Miles made a deal with his dad that he would attend the new school and stay there during the week, even though he could commute as they don't live too far away. In return, he is permitted to go home at the weekend.
Answer: Miles was touched by what Jeff said, and it inspired him to finally find the focus needed to control his powers.
TedStixon