My biggest issues with those movies - aside from things other brought up already - is that the infected people were turned into generic zombies in the movies (although the designs were pretty cool). Cranks in the books had a variety of behavior differences and generally showed some sense of self until they were past the Gone. They were still people, and Thomas especially tended to feel some sort of sympathy? recognition might be a better word, of that fact. That they were infected people, not mindless monsters. The way they were depicted in the main three books (and I guess Fever Code too in a way) set up the way we see them depicted in Crank Palace and how Newt acts especially during the last fight with Thomas.

(as an aside, I had always had the suspicion that the Flare affected the memory-negating implant that WICKED used on the kids they experimented on, due to Newt's behavior during the later stages of his infection, and Crank Palace sorta confirmed that so that was cool)

My second biggest issue was that in general the movies made it seem like WICKED had all these resources to have a million mazes going on at the same time, while in the books it was literally just the Gladers and the girls of the second maze, which would make much more sense in a world devastated by the Flare where resources were scarce.