I dunno, no matter how I look at it, the only way I can think of this is that the guy raped someone (most likely bully-girl). Sure, could have been consensual, but then there is no real reason to forget about him afterwards (they would still be there the day after) and the girl would not be left lying with her foot visible after he left nor would there be water left in the bottle.
Stain on the mattress? Obviously virgin blood, dunno how they ever thought cigarettes (do they think ppl try to light themselves on fire? And come on, it is literally a mat in a gym storage room. We all know what a stain in the middle of it is, even if it might have had nothing to do with the current mystery...). Him being seen on his knees? well duh. The water bottle is sus as all hell, and is likely drugged (the entire premise of evidence being left there in the first place is forced though), which would explain why the girl was left lying on the mat after he was done and had left. Bully-girl being so antagonistic towards the counselor and her family also makes sense, if she feels like they are callous people just covering up her plight.
Bunch of other things suggest this too (like him trying to keep friend-girl from letting anyone know he's there or otherwise getting help, etc.), but it was obvious enough from the moment we found out about the stain and that she saw him prone over the mat like that.
Honestly first "mystery" in this manga where the clues are actually proper and enough to prove something, and all the "deducing" from mc is not just very forced and not at all the only - or even most likely - possibility, and overall a huge stretch and discontinuous train of thought with tons of odd logical leaps.
