Factual error: When the bus is shown entering Washington, DC for the competition, the shot shows the bus traveling over the Arlington Memorial Bridge with the Lincoln Memorial in the background. That bridge is on the southwest side of the city. Since NYC is to the northeast of DC, this means that to get to that bridge and enter DC that way, the bus had to drive all the way around the city and then come back in from the opposite direction. Even if the bus driver made a mistake and missed the most direct route into the city from the north, there are dozens of other ways to get to the heart of the city without adding a good 45 minutes to an hour to the trip.
Factual error: The ferry splits in half down the middle, enough so the water is flooding in dramatically as the split grows. There is no possible way that the two halves of the ferry could have remained afloat like that. It would have sunk immediately. Then, as Iron Man "welds" the two halves back together, the ferry is afloat at the same waterline as before the incident, certainly not feasible with all the water it took on.
Continuity mistake: When Spidey first interrupts the criminals on the ferry, there are 2 motorbikes behind him on the left. When he throws one of the bad guys around with a web, the bikes have moved to the right, along with the yellow markings they were on, showing the shot's been flipped. They then move back.
Continuity mistake: In Peter's personal vlog of the airport battle from Civil War, he jumps in, grabs Cap's shield and immediately says "hey everyone." However, in Civil War he jumps in and grabs the shield without saying anything, Tony says "nice job, kid", there's a longer chat about the suit, and only later does Spider-Man say "hey everyone."
Continuity mistake: After Peter gets the text from Happy about meeting at the bathroom, Michelle asks, "What are you hiding, Peter?" and just as she says, "I'm just kidding I don't care," Peter's holding his cell phone up in his left hand, but next shot he's holding the cell phone up in his right hand.
Continuity mistake: When Ant-Man goes giant during the airport fight in Civil War, Peter is out in the airfield and reacts with a surprised "holy shit!" His video diary in Homecoming instead shows Peter hiding away from the action, and he reacts to the moment with a more subdued "aw crap, he's big, I gotta go now."
Continuity mistake: Near the start of the movie, Peter Parker is doing sit ups assisted by his friend. As the camera moves left, Peter is seen doing the exercise with both hands behind his head but as the camera then moves to a different angle he has both arms crossed over his chest with his hands at his shoulders.
Continuity mistake: When Peter and Ned are removing the tracking device from Peter's suit in the hotel in Washington D.C, Peter has a flashlight in his mouth. He removes it, but in the very next shot, it is back. Later, as he puts it in his mouth, it switches to his hand, and back to his mouth in between shots. (00:47:50)
Other mistake: A poster in the school states that the Academic Decathlon takes place on October 14-15. But later on in the movie, another poster says it's on September 14.