On March 18, 2016, it was reported that actor Dylan O'Brien was injured on set and was hospitalized. He suffered serious injuries when he was dragged under the vehicle to which he was strapped, while filming the opening train chase sequence on 17 March. His injuries included concussion, fractured cheekbones and orbital socket as well as lacerations. James Dashner announced via Twitter that the production was postponed after the accident. However, on April 29, 2016, when his recovery took longer than expected, production was shut down indefinitely. On May 27, 2016, 20th Century Fox rescheduled the film for January 12, 2018, allowing time for Dylan O'Brien to fully recover from his injuries sustained on-set. Production resumed almost a year later, in February 2017.
The take which lead to Dylan 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 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-Sangster wrote Newt's letter on his own. Director Wes Ball took it as souvenir from the set.
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 Dashner.
Ironically, the hardest and most dangerous scene to film - the opening train sequence - which caused the film to be delayed a year, wasn't even in the book.