Captain Obvious Reveal: What "choice-theft in the second degree" turns out to be. Possibly deliberate, as a way to show that Isaac, for all his intellect, isn't worldly enough to catch on that it's rape.
Mr. Motley is a powerful crime lord in New Crobuzon whose name befits his grotesque, multi-faced appearance. Mr. Motley regularly presides over assassinations, murders, and torture, with a knack for awful retribution to those who slight him — he's noted to send letters to those whose loved ones he holds ransom, having almost always killed them before he can be paid back. Obsessed with his own image, Motley commissions the Khepri artist Lin to create a statue in his exact likeness, and when he finds out Lin's lover Isaac is responsible for the escape of Motley's slake-moths, Motley kidnaps Lin and tortures her for weeks, possibly even raping her, and sending Lin's severed head-legs in an enclosed envelope to Isaac. Not even Motley's cheerful farce masks the fact that he's one of the most vicious characters even in New Crobuzon.
Mayor Bentham Rudgutter is the corrupt head of New Crobuzon, who inflicts horrific punishments on those he deems criminals, having them "Remade" into twisted forms, while also having them tortured or murdered in huge numbers. Secretly behind the murders attributed to the "Eyespy Killer", Rudgutter has dissidents killed, then their eyes harvested to replace his own pair. During the Slake Moth outbreak, he shows no compunction in having many people rounded up and killed, continuing these activities well after, even for rebel leader Jack Half-a-Prayer, with no amount of bloodshed too high to keep his hold on power. Oh, and the nearest thing he has to a "friend" is the handlinger-infested carcass that was once his second-in-command, until Rudgutter had his body usurped for plotting behind his back.
Ho Yay Shadrach and Tansell, the two men in the adventuring party hired by Isaac.
Idiot Ball: The first two times characters go up against the slake moths, their otherwise competent plans succeed in getting into position, but fail in in panic and disarray solely because no one thinks to Kill Him Already!.
Jerkass Woobie: Yagharek turns out to be a rapist. He is also one of the most decent people in the story, deeply remorseful and has had a pretty terrible life after his (admittedly deserved) punishment. It doesn't get better... it gets far worse. Even though he saved Isaac's lover and helped destroy the slake moths, when Isaac realizes his crime, he abandons poor Yag. He's so broken by Isaac's betrayal that he ends up mutilating his avian body out of shame, tearing out all his feathers, and commits to living in New Crobuzon for the remainder of his life as a man.
Moral Event Horizon: Kidnapping an elderly terminal patient and using him as bait to attract the slake-moths is an In-Universe MEH for Derkhan and Isaac. Derkhan comes up with several ways to justify the act, but rejects all of them because she knows there is nothing that can truly excuse what they're doing.
Squick: Dear God, anytime they mention Remaking. Especially the woman who has her baby's arms grafted to her face.
Tear Jerker: Lin's state by the end. Her human body is half-emaciated, bruised, and broken while her head beetle has had its eye crushed, legs broken, and wings ripped off, with which she used to show her trust to Isaac in the beginning of the novel. Even then, she is still happy to see Isaac after he had forsaken her. Also, Yagharek by the end.