I think she was pissed at him putting himself in hate way by the noteclear declaration, I did expect one of the two to come up with the notes as a reason for the meet-up, she was put in a spot and was unable to think clearly, or did not want to trouble him with a half baked lie and was stun locked from the rapid fire.
She needing academy help was a perfect excuse, wanting to keep it on the down low for her popularity works too, no one can say anyhting about it.
The gal was a bit dumb, if she thought the two were together and hiding it she should have proved it beforehand with pics instead of starting things in class without proof to spread the rumor she had a guy and hope her crush stopped being interested, hell, spreading pics of the 2 on the school social would have been more effective than becoming a heel in class.
MC and FMC talking in the library shouldn't create any new problem, everyone now thinks he is helping her with the studies, and they are just doing it openly instead of hiding it as the secret is out.