So judging by the comments rape has to do with him being on his "period", but how does tha...

There are indeed persons who have both..."reproductive organ" ...you know...hermaphrodites, or hybrids. So this could be the case. It's a bit like...omegaverse in real life^^
...or he's bleeding from the secual intercourse with the teacher...but for me it sounded more like he is hybrid. :)

I can tell you from experience tearing down their can be very bad. I had an ex that well... we experimented with me back there and neither one of us did much prep as far as stretching me... the one time it worked properly and I didn't tear it felt awesome but the other times when I tore.... bleed heavier than some of my periods and it was like diarrhea at the same time. One time I almost threw up and passed out at the same time while on the toilet. I didn't tell him that since it was afterward and I ran to the toilet and that's when the worst of it hit me but it was a horrible experience and I actually did wear a pad the one time it was the worst for the whole day. And that was from consensual... well I did start protesting when it hurt but mostly consensual sex. Imagine how bad it would be if it was rape and your around the age the kids in this story are. Corse most people's experiences aren't that bad so don't think this is common. Its good if you have the desire and patients to do it right. Anyways... So that may be TMI but I figure it would give you a idea of how rough it could be if someone was bleeding from that sort of thing.

intersex and on a period is possible as well although its not common in mangas that are considered yaoi so I'm not sure that's where the authors going with it. Would be interesting if that was the explanation for it though. I'd rather it be that than a case of rape and the kid being torn...

Its called being intersex