Contradictory phrases are the best, because sometimes they're the only way to describe something.
The overall story of The Scorch Trials is pretty dark. We have a bunch of kids being manipulated by people they can't contact, and most of the kids end up dying. And if they're not dying, their emotions are being totally messed with. Overall, this is a sick kind of torture going on—and even if the kids come out alive, they'll have major problems living the rest of their lives.
Nevertheless, the kids seem to take it in stride. Sure, their lives are pretty horrible, but they actually come to terms with that and are able to laugh it off every once in a while. Take Minho for example, the leader of the Gladers: "Hey, you bunch of sissy, no-good shanks! Grab all the food and get up here!" (17.47).
Of course Minho loves his fellow comrades, but he's also a total jokester, and his constant jocular attitude gives the story a much lighter tone.
But then there's Thomas, the Debbie Downer of the group—and our protagonist. We actually get to see his thoughts, and they're not always so happy. For example: Thomas knew Minho would've laughed his face off at that last comment, but to him it sounded like the saddest three words he'd ever heard (17.57).
The constant back-and-forth between lighthearted quips and depressing thoughts gives The Scorch Trials a surface that's littered when dark humor. That means that when you're reading it, you won't have to put the book down and mope around until you pick it up again, because even the most depressing scenes can be brought back up with a hilarious joke from Minho or Newt.
The Gladers' lives stink, but hey, a little laughter never hurts.