- Broken Base: The manga's character design is seen as really pretty or quite ugly.
- Die for Our Ship: Some people really have it in for Kureha...
- Ending Aversion: The ending upset a lot of different fan factions for different reasons:
- The people who were reading for the mystery arc thought that the final explanation was simply too silly and bizarre.
- The shippers were unhappy that Mashiro and Sou end up in the real world but with no knowledge of each other or memory of their love.
- The people who were reading for the exploration of ambiguous gender thought that the revelation that Mashiro's gender ambiguity is because they are actually fraternal twin foetuses sharing a mind meant that the situation was either reactionary or too fantastic to have any real-world relevance.
- Ho Yay: Between Sou and Mashiro, who doesn't belong to either sex but identifies as male. Sometimes. That's sort of the entire point of Mashiro's journey. And by the end, Mashiro identifies as female, full stop. Although it's less that Mashiro "identifies as female" than it is that the unborn sister kills her twin brother to gain full control of the single life they were sharing.
- Some consider Kureha x Mashiro to be Les Yay.
- Nightmare Fuel: Oh dear god.
- Values Dissonance: The way Mashiro's gender identity is handled can come across as offensive to some Western readers, to the point where a few actually stopped reading. And that's before getting into the problems with the ending that reveal Mashiro technically doesn't actually have "gender issues" because they're really two different people struggling for possession of one life, not one person struggling with their own identity.
YMMV / After School Nightmare