Were the movie written logically, Spider-Man: Homecoming's ferry scene would never have happened, and Peter wouldn't have gotten his suit taken away. In reality, both of those unfortunate events only occurred because genius tech inventor Tony Stark wasn't smart enough to send a quick reply to his protégé.
To elaborate, let's go back to the awkward argument between Iron Man and Spidey. Peter says "None of this would've happened if you'd just listened to me," to which Tony responds "I did listen, kid. Who do you think called the FBI?" Well, jeez, Tony, wouldn't that have been a nice thing to have mentioned to Peter beforehand? Honestly, young Peter Parker wasn't acting insubordinate and churlish when he boarded that ferry. He was simply doing his heroic duty because he thought no one else was going to. After all, with great power comes great responsibility (not that the movie ever mentions this).
All of the movie's troubles following the ferry scene, from Peter being stuck with his janky old suit to having to fight the Vulture solo, are a direct result of Tony's inability to respond to messages in a timely manner. A simple "Yeah, kid, I got your message, and the FBI are en route, so sit this one out" would've saved everyone a lot of headaches. Unfortunately, the world's most notoriously irresponsible billionaire playboy philanthropist just couldn't be arsed to do such a simple task.