Designated Evil: Esther's mercy-killing of the accidentally, mortally wounded bird, is presented as a cruel/heinous act. While it makes Esther seem like a Creepy Child, it's much more out of apparent cold pragmatism than anything inherently evil.
Esoteric Happy Ending: Given her overall incompetence and the fact John is now dead, it's possible Kate will not be allowed to keep her kids after the events of the movie. That said, the fact that Esther will have been proven to be something she totally wasn't could still make a difference for events moving forward though.
There's also this incredibly bizarre and dangerous cult, the Grail Movement, whose leader, Barbora Skrlova, has a glandular problem that causes her to look like a child, to the point she was able to legally change her identity to that of a thirteen year old named Anicka to elude authorities.
It Was His Sled: Esther being a 33 year old dwarf will catch on even if people haven't seen the movie thanks to the internet.
Jerkass Woobie: Danny starts out as a brat, but you can feel genuinely sorry for him. He's dealing with a psychotic adoptive sister who tries to kill him multiple times. Even if he was rude to Esther in the beginning, it turns out he was right about her.
Rooting for the Empire: It's easy to root for Esther despite the fact she's batshit insane because A) She's a great villain and B) Isabelle Fuhrman's performance. Not to mention most of the protagonists (except for Max) come off as whiny and annoying.
The Scrappy: John's stupidity, blind trusting of Esther, the revelation that he cheated on Kate after the stillbirth of their child, and myopia towards all the horrible events that had been occurring since she was adopted made him fairly unlikable to the viewers. That's why his brutal death comes and goes without much thought, and the rest of the film is dedicated to showing the much more charismatic Max attempting to survive Esther's rampage.
Strawman Has a Point: Esther's killing of the bird is supposed to be evil and heinous, but her correctly claiming that the bird's fate is Daniel's responsibility and that it's suffering and should be put out of its misery make it come off as cold but correct Shoot the Dog.
Esther, who is portrayed by an 11-year old, tries to seduce John in a sexually provocative cocktail dress.
Esther breaking her own arm, especially as the bone very visibly pops out. The fact that it's the only scene where she shows any real weakness or pain somehow makes it worse.
The entirety of Kate's Nightmare Sequence, if not helped by the completely sickening notion of witnessing a fetus removal from a woman's body.
This film's use of black lights. They reveal terrifying and disgusting, gruesome paintings, as well as sexually explicit paintings of John and Esther.
Sister Abigail's murder. When the police find her body, her face has been reduced to mush.
Take That, Scrappy!: Katie does give up on trying to convince John that there is something wrong with Esther and say if he wants her to leave that's fine but only on one condition that Esther goes too which is pretty much satisfying.
Kate, who has just lost her baby, is mentally abused by her adoptive daughter for the length of the film and is hospitalized when her (perfectly justified) paranoia causes her to assault Esther in public.
Max has it worse. She is a 5-year old mute child who witnesses her new adoptive sister brutally murder an innocent nun and her own father, is almost killed herself in at least 4 separate occasions, sees her brother nearly burn to death and be suffocated, is chased by a psychopath into the woods and is forced to handle a firearm despite her young age. It's safe to say that the trauma from her childhood will haunt her for the rest of her life.