Continuity mistake: There are missing boys along 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.
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.