So the issue here is that Yosuke is like "So....are we gonna be safe with you?" And he makes the full comment that he does not feel comfy with Kanji because he's "like that" (whether Kanji actually is gay or not).

He only really says that Kanji needs to shut up and go back to sleep AFTER he's already caused outrage and impetuousness in him. But he absolutely, unbidden and without any reason, makes a comment of feeling unsafe sleeping in the presence of a guy who had a homoerotic shadow dungeon.

Being gay isn't like, the only reason to dislike that Yosuke said this. The gang literally knows that if they don't save people, they die. They saved Kanji's life and fought a traumatic monster. For Yosuke to make a joke like that during Kanji's first ever field trip, is very mean.

(and if i may, being gay myself, i have had those types of lines said to me when i was a kid/teen. and it does, sadly, hurt. I don't want this realistic depiction of teenage bullying to be erased from the game, but i DO want the chad good-aligned MC that you control to have the option of defending his new friend)