These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Base: The announcement that Uriah will be cut from the first movie and saved for the sequel. Some believe that Uriah's purpose in the first book wasn't that important, while others that love the character still call heresy on it. Basically, it's Tom Bombadil all over again.
Molly is described in-text by Christina as the kind of kid you'd see torching ants on the sidewalk, too.
Also, Erudite's leader, and the main antagonist of the book, Jeanine. She engineers a revolt against the Abnegation-ruled government by mind-controlling all of Dauntless, resulting in countless innocent people killed.
Considering the reaction to his character being cut from the first movie, Uriah seems to be this.
Hollywood Geography: Dauntless territory apparently stretches from the Hancock building to Navy Pier, among other inconsistencies.
Moral Event Horizon: Peter crosses this so many times, it's hard to keep track. Shining examples are how he stabbed Edward in the eye while he was sleeping. Then there was the time he hung Tris over the chasm (claimed it was just to scare her) and groped her chest, while mocking her.
For Caleb, betraying his family to the Erudite. The full information about the outside world and what Jeanine told him has yet to be disclosed. But regardless, it doesn't change the fact that he sided with the faction that killed his parents and helped with the capture and attempted execution of his own sister.
Take That, Scrappy!: If Peter, Molly, and Drew do something to irritate you, just breath a sigh of relief that they'll be humiliated for it later by Tris' hands.
Marcus gets one in Insurgent when Tobias gets laughed at for fearing him. So, to prove that he's no coward, he gives Marcus a well-deserved beat-down.
The Woobie: Four. He's actually an Abnegation transfer named Tobias who left because his father, Marcus, constantly abused him.
Of all the book's characters, Al is the king of this trope. He spends his nights crying and shuddering in fear, despite being one of the biggest and strongest of the Dauntless initiates. He develops a crush on Tris, but she never returns his feelings. Finally, he is pressured to join in on the attempt to kill her, because her success made him feel weak. Later, after tearfully begging for her forgiveness, he is met with a callous and heartless rejection. Unable to live with the fact that she could not forgive him, he kills himself.
YMMV on whether all of those things were not well deserved. Tris had no obligation to forgive him after he almost murdered her with the excuse that "her success made him feel weak". Nor did she have any obligation to reciprocate his feelings, and she did do her best to let him down easy.
Tris is one after the end. She is bullied and harassed constantly for being a "Stiff", watches her entire world and society crumble around her, is forced to shoot one of her friends (who was mind-controlled), loses both of her parents, and is nearly shot and killed by the boy that she loves.
Trauma Conga Line: From the ending of the first book onwards, almost every character crosses this.