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- Dylan O'BrienDylan O'Brien suffered serious injuries was dragged under the vehicle to which he was strapped, while filming the opening train chase sequence on 17 March 2016. His injuries included concussion, fractured cheekbones and orbital socket as well as lacerations. The recovery took longer than expected, which resulted in the production shutting down indefinitely until he fully recovered. Production resumed almost a year later, in February 2017. Ironically, that scene—the hardest and most dangerous scene to film—wasn't even in the book. The take which lead to Dylan O'BrienDylan O'Brien's head injury was used in the film, when Thomas jumps from the window of a moving car as it approaches the WCKD train. Wes BallWes Ball, who revealed that it was the longest shot of the sequence, asked O'Brien's permission to have it included in the film, to which O'Brien responded, "I need you to, in a way. I would be more heartbroken than if it just went to waste." After the incident, Ball decided to no longer shoot with a moving train and opted for a parked one instead, with effects from WETA giving the illusion that it was in motion.
- Thomas Brodie-SangsterThomas Brodie-Sangster wrote Newt's letter on his own. Director Wes BallWes Ball took it as souvenir from the set.
- Kaya ScodelarioKaya Scodelario (Teresa) proudly performed her own stunts for this film.
- As a joke, the memorial that appears at the end also contained names of several crew members as well as director Wes BallWes Ball and lead actor Dylan O'BrienDylan O'Brien.
- In the Book, it's revealed Brenda and Jorge were working for WCKD; this is cut in the Movie.
- In the book, they actually go back inside the Maze, and jump in a portal that takes them to the safe haven, and Thomas never gets shot.
- Despite prominent billing, Nathalie EmmanuelNathalie Emmanuel, [?] Jacob Loftland and Katherine McNamaraKatherine McNamara have less than 10 minutes of screentime.
- In the movie, it is shown that Thomas' blood contains the cure for the flare virus. In the books, it is neither his blood that is the cure nor a definite fact that he could be used as one. The scientists instead try to convince Thomas to give them his brain in the hopes of finding a cure with deeper investigation.
- There's a scene where Teresa and Ava are presenting their data to board members at WCKD. One member, the only one not to speak a word, is none other than that author of the book series, James DashnerJames Dashner.