Dylan O'Brien suffered serious injuries when he was dragged under the vehicle which he was strapped on when he fell on top of its roof 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 had to be shut down indefinitely until he fully recovered. The production would only 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.
When the audience is first introduced to Lawrence, he is heard muttering "Rose took my nose I suppose." This is a reference to an event from The Scorch Trials book that didn't make it into its respective movie; in the book, while Brenda and Thomas are trapped in the tunnels underneath the ruined city, they encounter and are chased by a Crank who says "Rose took my nose, I suppose."
Towards the beginning of the movie, there is a scene in which Thomas, Newt, Frypan, Brenda, and Jorge stand at an overlook and see The Last City for the first time (as seen in numerous trailers and TV spots for the film). The musical score that accompanies this scene is actually a piece of music called "Memories" composed by John Paesano for the video game Mass Effect: Andromeda (2017). Paesano, of course, also composed the music for all 3 films in the Maze Runner trilogy; thus, his work for Andromeda is simply reused here (and receives proper documentation at the end of the film's credits). Fans will notice that as the scene transitions to an aerial shot of The Last City, the horn-piece that can be heard in this shot is indeed the main recurring theme/motif heard throughout Mass Effect: Andromeda.
Branda's hair is more similar in length to how it was in the book, rather than being short like in the last film. It was most likely done because Rose Salazar (who plays Brenda) was filming Alita: Battle Angel at the same time as this, which required her to have longer hair.
During the opening train rescue scene, the Maze Runner theme (composed by John Paesano from The Maze Runner (2014)) can be heard twice; firstly when Thomas is calling for Minho, and secondly (and more dramatically) when the Gladers and Right Arm have successfully lifted the train car. However, track 1, "Rescue", of the officially released Death Cure soundtrack only features the second, more dramatic appearance of the theme; the first appearance has been cut out. In addition to this, the Maze Runner theme also appears during the credits of The Death Cure, the same way it appeared in the credits of the previous two movies.
On March 18, 2016, it was reported that actor Dylan O'Brien was injured on set and was hospitalized. James Dashner announced via Twitter that the production was postponed after the accident. However, on April 29, 2016, production was shut down indefinitely as O'Brien's injuries were more serious than previously thought.
It is hinted in the second Death Cure trailer that the film will follow Newt's original book ark. This is seen by the black veins visible on his neck, and the bags under his eyes. In the book, He begins to turn into a Crank due to his blood not having immunity to the flare and Thomas must kill him before he fully turns.
In the Book, Minho is Never captured at all, it's actually Newt who gets Captured half way through the Novel, resulting in them having to go to a place WCKD keep Cranks locked up to rescue him, a scene completely cut from the Movie; a similar scene however happens when they get attacked by the Cranks in the Tunnel.
Ava Paige plays a much bigger part in the film series, while in the books she was simply a mysterious character that wrote notes serving as epilogues for each novel. She also didn't die in the book, or at least her death is not written explicitly.
In the book, Thomas kills Janson in a fist fight, similar to how he took out Gally in the First Book. However, Much like how Gally's "Death" was changed, Janson is killed by Crank test subjects in the film.
Due to events changed from book to screen in the previous movie, Thomas does not hate Aris at the beginning of this movie, in fact, he's glad to see him, unlike in the book where couldn't trust him anymore similar to Teresa.
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.
Everyone is Captured at the end of The Scorch Trials Book, not just Minho, and it was done more deliberately, as in they agreed to go with WCKD rather than being taken against their will. Their Ensueing escape at the Beginning of the Death Cure Book is pretty similar to their Escape in The Previous Movie.
In the book, when Thomas and his friends enter the city (which is not walled off in the book, unlike the film) they get a letter from Gally telling them he's alive and to come meet him. In the Film, he happens to be at a protest rally at the same time and saves Thomas & the others from being found. This was done to probably make it a more visual reveal.
Only a small part of the book takes place in the Last City (as the film puts it), the book jumps from location to location, from the City, to a place WCKD keeps cranks, to the climax being set in another Maze.
In the Death Cure Soundtrack, the track played during Newt's death is the latter part of "Please Tommy, Please" (by John Paesano). This is actually a variation of the track called "Finale" in The Maze Runner (2014), played during Chuck's death.
In the first film, one of the tracks in the soundtrack is called, "Goodbye," when the Gladers are leaving the Maze, as in they're saying goodbye to the only home they've known. In the second film, there's another track called, "Goodbye," and that's with Winston's death, as in goodbye to a friend and it's basically showing the Gladers that survival is their best option. And in the last film, the last track is also named, "Goodbye," as in, goodbye to the series.