There are continuity and logic issues with the film, but like many films, I can let them pass because I see them as light entertainment. Which is not to say Marvel Studios couldn't try harder; but overall they deliver a lot of fun.
Vulture and company were a little flippant about the murder of Shocker #1, but we don't know how deep these guys were, 8 years later. Even in the opening scene, we see that Vulture has a history of violence by the reaction of his crew before he swings, and he didn't look too fussed about having guns pointed at him.
The lack of armed response to the jet being compromised -- in fact the lack of armed escort -- did take me out of it a bit.
I didn't love the end fight, but as I've mentioned, I seldom do.
Flash's race is irrelevant to me, but I think he could have been more physically intimidating. Now that being said...he clearly came from money, which would explain a lot of his arrogance and status.
In Civil War (and some of the Homecoming scraps) Spidey was more capable, so I think they overdid it when they played his inexperience for laughs, but hey -- I laughed.
Just for the sake of being iconic, I can agree that I'd like the real (future?) MJ to be a sexy readhead, but beyond that I'm not too fussed about May's age or any of the supporting cast's race. I loved the big twist involving the 'dear old dad' reveal and don't have issue with how it was enabled.
In Civil War Peter wasn't familiar enough with ESB to know what AT-ATs were called, but geeked out over Lego Death Star in Homecoming. That was fast.