In the books there was only one other maze with all girls and Aris. In the movie there were multiple mazes in comparison to the two in the books.
In the book the Gladers refer to Janson as the Rat-Man. It isn't until The Death Cure that we learn Janson's real name.
Body Count 2: Winston and Mary Cooper.
In the movie the Cranks are seen as zombies, but in the books they are actually just people who have gone insane. The Flare does not kill you right away, but slowly makes you go more insane until you lose control.
The director Wes BallWes Ball says the movie will diverge from the book a little bit, but will get back on track in the third installment titled The Death Cure.
Brenda mentions that her brother was taken away from her, his name was George. In the Maze Runner, Thomas stop at a grave with the name George on the tombstone. It is safe to assume that the grave was Brenda's brother's.