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: Kaoru's and Sentarou's bromance can come off as this.
Kaoru: "What will you do" (blows in Sentarou's ear) "... when she does something like that to you?"
It doesn't help that Kaoru openly admires how good-looking Sentarou is. Or how fond this anime is of making him blush at any opportunity. Plus, the relationship drama is really strong in this series, so they have a really emotional friendship. Then Kaoru throws a fit when Sentarou starts hanging out with some other guys from their class. And then there was that scene where Sentarou pinned Kaoru to a bed...so yeah, even though the both of them have or have had in Sen's case female love interests, this is pretty much what got the anime a good percentage of its viewers.
Misaimed Fandom: Thanks to the above, there were many a viewer who assumed this series was BL.
MANY a viewer, especially around the time that the anime was announced, thanks to people being somewhat unfamiliar with the series, and much of the anime's advertising (and the OP sequence) focusing very heavily on the two main guys.
Tear Jerker: Sen telling Kaoru about his childhood causes Kaoru to start crying, half because he felt like an ass for thinking his life was so bad, half because it was just plain sad.
The episode when Kaoru meets his mother for the first time. Especially at the end, when she starts crying as he's leaving and mouths "I'm sorry". He shakes his head, to show that he is not angry at her for what happened.
The Gray Rain of Depression that occurs when Kaoru learns his father will not be able to stay for long when he returns home.
The flashbacks shown when Kaoru remembers being rejected by friends in the past.