Deliberate mistake: Despite taking place for at least three years (prior to the arrival of Thomas) in an isolated post-apocalyptic setting, the boys in the Glade have professional looking hairstyles, not the least of which are Minho and Gally, who both have short hairstyles that look evenly cut and professionally maintained.
Continuity mistake: Thomas takes the blade of Theresa at the top of the tower. When he does, his grip on the blade changes position and the hand changes too. (00:55:30)
Continuity mistake: After Minho and Thomas escape from the blades of Section 7, they are crawling through a small passage with the ceiling coming down on them slowly. In one shot, the ceiling is touching Thomas' back. But in the next shot as they get out, he still has a few inches of clearance.
Plot hole: At one point it is mentioned that they have tried everything to escape the maze, and that it is impossible to climb up because the ivy doesn't grow all the way to the top of the wall. Yet in the aerial shots the ivy is shown reaching the top of the walls.
Continuity mistake: When the Griever "drools" on Thomas for the first time, it leaves a big visible trail of drool/slime. Camera cuts and the big visible trail has disappeared instantly. (00:37:00)
Continuity mistake: Ben gets hit round the head with a stick and blood appears. However when they start to carry him to the pit, the blood disappears in some shots. (00:22:30)
Revealing mistake: When Thomas is running through the blades to rejoin the other runner, as they run into each other it is a CGI background. (01:08:50)
Chosen answer: As it turns out, Gally was being mind-controlled by the people who operated the maze. This would explain why he was highly against any form of escape plan. When the others escaped, the operators gave him some form of safe passage straight to the control room.so he could kill the others. Best guess is, they re-activated the elevator for him and he took that route...but that's left ambiguous.