Henri's remark

Before the scene where Francois and Serge have sex, they have been meeting at nighttime in Francois' room and in other places in the dormitory - or at least that is suggested. As Serge is Henri's roommate, he notices the absences, also notices that they are friendly with each other (note the scene where he barges in on their meeting outside of the classroom), and it appears to bother him somehow - even suggesting he is jealous (he is an alienated outsider). Henri has also picked up on the fact that Francois is gay. So, Henri just puts two and two together and probably guesses that they have been up to something. If he actually saw something, it was probably just that they were laying there side by side talking, as they did before the "seduction" scene.

Um, don't you remember? There was a scene before the sex scene when Bartolo visits Francois for the first time and asks him if he wants to smoke on the rooftop. Bartolo visited him to get some help with his essay in French class, and this is the scene that Henri was pertaining to.

Well, we can assume that since Henri and Bartolo were originally roommates, and that Henri rarely sleeps, he noticed during this one instance that Bartolo left the room and went off somewhere. However, the subsequent scene when Francois and Bartolo both ask the teacher to be excused to the toilet whilst giving each other extensive looks in class, probably gave Henri reason to just check them out a bit. And so given his "experiences" (this is kind of unclear) with other men that sleep with men when he lived in Paris for three years, he probably assumed that the same thing was happening between Francois and Bartolo.