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.
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.
Unfortunate Implications: Considering this is a manga about a hermaphrodite facing his/her fears and dealing with his/her sexuality, you would think that its stance on gender roles would be quite progressive. For the most part, this is true. Sort of. It's understandable when Mashiro defines what a man and what a woman is through stereotypes since it is his/her learning that those idealizations are just stereotypes that allows him/her to grow in the manga. It's less understandable when Kureha realizes that Mashiro actually wants to be a girl because he/she slapped her and "A man would never hit her".
Then there's the whole issue with Sou. On the one hand, Sou does a great job of making Mashiro realize his own inner desires to be a girl through loving him. In fact, Sou is able to make Mashiro not only come to accept himself and possibly love himself, but also accept and love others. However, Sou's tactic? To constantly subject Mashiro to his masculinity, ridicule Mashiro's sense of manhood, continuously play up Mashiro's femininity and submissiveness, and basically forcing Sou's own desire for Mashiro to be a girl on to him. Sou makes it more than clear that he loves Mashiro, but only sees him as a woman and only loves her as such.
Even that could be seen as unfortunate if you have an Alternate Character Interpretation of Sou. Is he really a guy that saw Mashiro's inner femininity, fell in love with it, and wants to draw it out to the surface or is he a guy struggling with his own sexuality that cannot accept being in love with a man and therefore forces the man (who is conveniently a hermaphrodite) to become a woman? Viewed as the latter, Sou becomes a sad example of homosexuality portrayed in the media.