When driving next to the train. Camera goes in the machine room where they spot the car directly to the side. When the camera switches the car is quite a bit behind the machine room.
When the main characters like Thomas Brodie-Sangster, Dylan O'Brien, and Ki Hong Lee jump from a building, they land in the water and they climb out dripping wet. In a following scene, moments after, their appearance has changed from soaking wet to barely damp. Their tactical boots should also have squelched for a long time, as wet boots do, but not a squishy sound to be heard.
Twice in the movie walkie talkies are used while far away from any receiver. Walkie talkies, like cell phones, require a repeater transmitter to communicate long distance, unless another unit is within sight.
It is impossible those would have been within range as intended in the movie.
At the end, before Thomas throws the tank at the glass to let the "Cranks" out, instead of yelling Janson he yells Jason.
When the Gladers are exiting the upside-down truck, in the tunnel with the Cranks, Thomas puts his hand down hard, right on a sharp triangular shard of glass in the truck window, and no damage is done.
In the background of the scene where Ava and Theresa meet in the hall way of a building, you can see a South African flag out the window on the right. That is due to this being shot in South Africa at the Cape Town International Convention center.
When the VTOL goes to the top of the WCKD headquarters they bank right to turn right. That is seen from the cockpit. The horizon instrument stays horizontal compared to the plane but it should move to be aligned with the actual horizon. The cockpit instruments are a still picture.
At 30:43, the windshield is punched but the crack appears centered away from where the person punches.
Just before the cure is applied to the little girl at WCKD headquarters, a square reflection of the camera is seen in the eyes of the girl when she is laying on the medical table with the lights above during a close-up of her face.
When Thomas is listening to the speech to the just rescued kids at the shipwreck yard in the beginning of the movie, you can see movie equipment like a TV monitor reflecting in his eyes.
When at the coastal encampment while looking at the map to the "City," the city circled on the map is where Denver is located. After Thomas and the others are rescued from the tunnel, Jorge remarks that they almost made it a whole day. Then, during that conversation they come to a stop outside the "City" in question. They appear to have driven from the Pacific coast to Denver in the same day, a drive of over 1,000 miles.
The Gladers made an obvious tactical error for no reason. In the opening scene, during the assault on the train, the Gladers manage to hijack a Berg, separate the back half of the train, and take out five of the eight members of the train's security force without any Glader being hit. At this point, with superior numbers AND the Berg's additional air support, they decide to flee the three remaining security people by precariously airlifting a train car full of prisoners with five Gladers clinging to its roof. With superior numbers and air support, they could have easily overwhelmed the remaining three, collected any valuable equipment and weaponry, then continued on their merry way.
Paige tells Janson there are 28 immune kids left. Some scenes later, Teresa tells Minho that there are 28 kids left besides him. That would make the total 29. Either Paige or Teresa is wrong.