Peter says he is under 21 when Beck offers him a drink. Based on his age during Captain America: Civil War he should be 17 or 18 now. The legal drinking age in the Czech Republic (and most other EU member states) is 18.
When MJ finds Peter on Tower Bridge, they share a long hug. Peter's face is bleeding and in the wide shots the blood transfer to MJ's jacket, left shoulder, can be seen but in the close up shots the blood is absent.
When Peter gives the glasses to Beck, he has to go through a transfer routine with Edith -- however, when Beck gives them back on the bridge, Peter just puts them on and Edith responds without any required transfer protocol.
During the attack in Venice, Peter gets soaked when the water pushes him against the railing. Moments later, when he retaliates against the water elemental, his clothes are completely dry and his hair is slightly damp.
When the Stark Jet enters the UK, the caption states the Dorset coastline. Flying from Amsterdam to London you would cross the eastern coast of England, entering over the coast of Essex but the Dorset Chalk Cliffs are on the South West coastline which is 160 miles away.
The Dutch village of 'Broek op Langedijk' is actually the courtyard of a Prague restaurant, which explains the village's typical Central European style of architecture. The actual village of Broek op Langedijk is located just north of Amsterdam and is known for the many agricultural canals that intersect the village.
The scene where Peter is sitting on Charles Bridge with Mysterio shows the bridge at least one level higher than the adjacent bridge. Both adjacent bridges, Mánes Bridge and Bridge of Legions are in the same level as Charles Bridge.
Based on the shots in the scenes both prior and after, the students are staying at a hotel on the main island of Venice. When they depart, a bus picks them up. However, in reality, motor vehicles are not allowed in the city, especially not buses or coaches. It would be impossible for them to navigate the winding streets or canals.
This film succumbs to the now very tired goof of hand guns making metallic clickety noises as they are raised. Apparently sound people believe the audience needs to hear this and is supposedly the sound of a safety being removed. Except, the hand guns making the sounds are Glocks which have no external or manual safeties. They do not make any noise.
Multiple errors relative to European trains. Spider-Man is shown hopping atop a high-speed "bullet train" from Prague to Berlin, and later inadvertently ending up on one from Berlin to the Netherlands. There are no bullet trains at all in the Czech Republic, and none that directly connect Berlin to any destination in the Netherlands - certainly not to the small town where Spider-Man ends up. Additionally, a train driving through Berlin would not have the speed shown in the film. Further, his classmates appear to travel from Prague to London via train. There is no direct train route of any kind between the two cities, and it would take nearly a full day of travel to connect through a minimum of four stations en route.
The train from Prague to Berlin is a RailJet Express, which doesn't go with a locomotive we see in the movie. RailJet locomotives are newer types, with a painting that fits the rest of the train. The one in the movie has the classic Czech Railways painting, not used on RailJet trains.
The train that departs from Prague uses thousands of Volts electricity, starting from 15000 V. There is no way Peter would have survived the trip from Prague to Berlin on the top of the train, as electricity of this voltage is lethal even from a certain proximity, without even touching the cable that's right next to Peter.
The license plate of Nick Fury's car in Berlin is MTU 83779. While this combination has a meaning in the wider sense (see trivia), it is invalid. MTU is not registered for any German city/county and this specific combination of letters and numbers (ABC 12345 instead of the usual AB CD 1234) is reserved for official use only. Additionally, the front plate has the sticker for the emissions test which is not issued anymore since 2010.
Ironically, the actor playing the helpful Dutchman who offers Peter Parker to pronounces the name of the village ('Broek op Langedijk') he's in, is Czech instead of Dutch and mispronounces the name himself as well.
Peter explains to MJ that he gave the glasses "again" to Mysterio. Peter only gave him the glasses once, even though Quentin did originally have a pair he helped develop with Mr. Stark, Peter does not know this at this point.
The main weapon used against Spider-Man are drones with projectors. The technology uses light to project an image. Light isn't a solid, so even if it projected a shape, you would be able to see inside it to see the drones. Spider-Man goes inside the image at one stage and he can see the drones in a battle scene, again suggesting the image has a solid surface you cannot see through with an inside and an outside.
Light just doesn't work like that. It isn't a solid, and has to be projected onto a solid to see it being reflected (like a movie screen) or refracted (like a rainbow). But even rainbows are transparent.
Nick Fury mentions that Dr. Strange is unavailable when Peter asks about him. However, in Thor: Ragnarok, Strange makes it clear that inter-dimensional crises are his top priority - surely the Elementals would be relevant enough for Strange to at least consider investigating.
The goof item below may give away important plot points.
There is no possible way that Quentin Beck could have successfully kept up the lie that he was a superhero from another dimension, especially not after his own death. Assuming that there were some employees at Stark Industries that did not join up with Beck following Stark's death, they would have been able to recognize him as one of their fellow co-workers; also considering how he invented that holographic technology, he would have held an extremely prominent position (even if he didn't take credit for BARF). Plus, after his death, SHIELD would have shared Beck's known info with other officials so that they could work together to do as much research on him as possible (just to ensure he doesn't have any additional criminal activity). This being the case, there would be too much evidence to prove that Beck's broadcasted video in the Daily Bugle is completely fraudulent.
The final twist about Peter's identity is possible only if SHIELD kept Mysterio's activities a secret. SHIELD, or the Skrulls who impersonate them have no reason to do so, especially as Peter sabotaged the hologram trick of Mysterio, and that certainly went viral in the age of smartphones.