I think it's more of her experience with other men which causes her prejudice for men
She said that she comes across pervy men on the train station frequently when she doesn't go early in the morning so I guess her brain adjusted to thinking 'all men are bad' as if it were a fact, but since Yuki-san seems and acts like a girl she forgets that Yuki has a gender. And for Kei-Kun's side, it seems like Mayu thinks he's scary since he looks at her a lot, well extra scary to be exact since I'm pretty sure she thinks all guys are creepy one way or another, if she were normal she would most likely ask her best friend if Kei hates her especially if the best friend and the guy in question are friends, well unless the reason you think he hates you is because you hog your best friend away from him.
Anyway, that was just a conspiracy, and it's probably false since it's a fictional story that probably doesn't have an explanation it's self