Continuity mistake: There are missing boys in the movie. At the end of The Maze Runner, there are 8 boys that get out of the maze besides Teresa. At the beginning of Scorch Trials, only 7 get in the compound. When Thomas shows the stolen card to the others, there are 6 of them and they all escape with Teresa and Aris. When they get out the mall and enter the city, there are 5 of them besides Aris and Teresa. The last boy (called 'Jack' by cast and crew) dies in a deleted scene, the other two boys simply vanish without a trace or explanation.
Continuity mistake: The woman who delivers the blood sample at the beginning of the third scene, changes outfit/character when placed onto the table. (00:08:00)
Character mistake: Near the end of the movie, when Newt and Minho and Frypan and others are all being checked by WCKD's scanners to identify the subjects. Minho is called subject A4 when he is really subject A7, subject A4 is Chuck. Newt is also called subject A6 when he really is subject A5, Subject A6 is ALBY.
Revealing mistake: When Tomas and Brenda are avoiding the big pile of stuff down in ground in the elevator, there are wires visible pulling them.