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.
Fridge Logic: The question of where Armada gets its fresh water is never addressed. The scarcity of drinkable water on the Therpsichora is mentioned early on, but there's no indication that Armadans use desalination techniques, or even set out catch-basins during rainstorms.
Ho Yay: There was a mix of this and Foe Yay between Uther Doul and the Brucolac. Mostly from the Brucolac's side. He very explicitly wonders whether Uther is a masochist, and then acts like a scorned lover through most of the novel. There's also the matter of what exactly their history together is. This pairing isn't invalidated by the ending, either.
Offscreen Moment of Awesome: The book's largely about a narrator 'lost at sea' in a city that's often outside the bounds of her knowledge and understanding. The story builds up a rivalry - and an intriguing past acquaintanceship - between two overpowered badasses, and they finally get their showdown a couple of chapters from the end...but then the fight scene gets skipped entirely, and instead we get to see the aftermath at the start of the next chapter.
Unfortunate Implications: For "The Scar": Bellis is an uppity woman, who seems to get her comeuppance and becomes humbled by the end.
Very much YMMV; Bellis develops from being a complete Tsundere/jerk into a more likable character because she actually starts to aid and care about others; she's very competent and holds her own in most if not all situations. She's not so much humbled as more experienced, and only as traumatized as EVERY. SINGLE. MAIN. CHARACTER. that Miéville writes. Note the kid whose story could be equally argued to be saying that literacy will inadvertently lead to death. The guy manipulating Bellis was a master spy who pretty much managed to singlehandedly infiltrate the entirety of Armada, and only got taken down by Uther Doul and the Brucolac. See above, under 'Badass' for the two of them.