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.
YMMV: Centaur no Nayami
Ensemble Darkhorse: Its hard to pick just one, but the Class Rep and her family are a pretty big one, as well as Shino-chan. The Antarticans and pretty much everyone who isn't one of the main three.
Hollywood Pudgy: Himeno is constantly worried about her weight, despite the fact that a non-Centaur would likely not notice it at all. Justified however, given how Centaurs will have serious hygiene problems if they become over-weight.
Les Yay: There are obvious examples, like the openly-lesbian relationship between Akechi and Michi, while some are implied like Himeno's mom and her angel classmate from high school, and of course Nozomi and Himeno.
Ayaka also has a huge crush on Hime that she seems blissfully ignorant of.
Omaki received a "thank you-kiss" from Manami when they were in elementary school. The former still has feelings for her. They even go on a "date" in chapter 46.
Akechi and Michi had already sex, as revealed in chapter 31.
Pacing Problems: A rather unique one: occasionally, the manga doesn't do scene changes very well, leading to abrupt segueways and often a case of What Happened to the Mouse?. The lack of dialogue in many of these instances does not help matters.
In the human-faced dog side story, there's a sudden jump from the dog running to get help (and being terrified of the outside world) and her owner waking up in hospital. We're never shown where the dog went or who it sought help from. In addition, the rest of the owner's family (other than her abusive mother) appears out of nowhere. Not only is the reader left to figure out what's happened, they're left to guess who these people are.
In Chapter 8, there's an abrupt shift between Himeno debating whether to do an archery ritual, and one of the Chi siblings being held hostage. All we get is a shot of the shrine gate and a crashed car - no context, no foreshadowing, and no explanation of who the criminal is or how he got a hold of the child.
Viewer Gender Confusion: The fan translators first thought that Omaki (a Cat Girl) is a "he". Even when she wears the sportswear, you can see that has breast (they are not big, but visible enough).
What an Idiot: Hime's classmate Fujimoto, in charge of the props and sets for the class play, is convinced that the tower prop can bear Hime's weight because he tested it by getting Nekomi (the fattest boy in the class) to jump up and down on it, saying that "she can't be heavier than Nekomi-san, right?" Somehow he failed to consider that, since Hime is a centaur of COURSE she's going to be heavier than even the heaviest biped in the class! Predictably, it collapses during the performance.