Nah, basically Komaru is changing in Naegi's room. Naegi's saying something like "Why don't you change in your room?" and Komaru is more like "Who cares, we're siblings so it really doesn't matter" and some reason for why she's forced to do it there.
Of course, when Fukawa enters the room she basically sees Komaru undressing and Naegi laying on the bed without his jacket, so yeah, total misunderstanding. Specially since she believes Komaru has a brother complex (seen in the game).
Btw, about the fact if Komaru is really or not a brocon, I am not sure. Honestly, the game only shows that they get along well and that's it. Fukawa says she said Oniichan while she was sleeping but she could be lying or be one of her dellusions, which I wouldn't be surprised.
But honestly, a girl her age still calling his brother Oniichan is really weird honestly, specially with that little age difference.