I saw it as him associating that not being comfortable enough for sex = SHE DOESN'T REALLY LOVE YOU, which makes me feel "eh". Aren't "nice guys" supposed to like, aim for being loving, understanding and supportive, but instead he was like "it's okay, you don't have to force yourself, *pained face*, *stops talking to her for the rest of winter break*". It irks me, that unwillingness to have sex correlated with "she's not into you". Ofc it's always a possibility, but he made a leap and stuck with it and just pouted like a kid for weeks.
Not trying to defend him or anything, but I don't think it was only because of the sex. He had probably picked up on Yuma's vibes too and sex was the most tangible proof.
Sure, he didn't handle the situation the best, but this is very common with people that may not have bad intentions but end up screwing up because they don't know the right way to do it.
I don't think Yuma liked Takeda in a romantic or sexual way. She liked him as a friend and someone nice to hang out with. So she thought, since he was a guy and she was supposed to find a bf, this meant she might like him in that way too. That's why, in the first chapter he asks her "When it comes to us, what is the difference"
If Yuma liked him that way, she would do it. She does it with Hotaru because she likes her. I don't think Hotaru is manipulating her this time now.
Anyway, this type of NTR is only bad because of the abuse parts. It is not angsty on an emotional level regarding the third people (the guys) because neither Yuma nor Hotaru have actual feelings for them. It's not like KnM or WDTFS where there are actually feelings for two people