Well, I can think of some "legitimate" plot holes. Like the fact that Vision took down War Machine because he was "distraught" (I don't know how they say it in English, that's the literal translation from the Spanish version), but back when he tried attacking Falcon there was literally no thing that could distract him that moment. It was just some plothole convenience so that Captain America could escape.
And I don't know if it counts as plot hole or as a really, really poor plot device, but there's no reason why Tony Stark should know Spider-Man's true identity. There's none given, unless watching youtube videos is proof enough. Which in itself makes no sense, why bring Spiderman to the fight when he has no real reason to be there? He's just so that Marvel screams to the audience "hey, we got him back!"
Then there's just some flaws or the magic coincidence fairy that was also present on The Force Awakens here, like a camera on the middle of nowhere ready to film Bucky killing Tony's parents (had the car steered a little bit more and no footage would have been found!), Captain America knowing this information...because I don't know, frankly, how did he know about this? And how did the evil guy know that Iron Man would show up with the Winter Soldier to show him this footage?
Not hating on the movie, by the way. I enjoyed it much more than I thought I would, and these flaws didn't affect my perception on the overall scheme of things. But there they are, regardless of the situation!
