Another possibility is that she had an argument with a friend. It might not even be Ron. It could be with Harry or another Gryffindor. She's very sensitive about her friendships and any conflict could make her cry.
Perhaps Hermione is facing some sort of interpersonal issue. She could have had an argument with her friends, like Ron and Harry. In the wizarding world, friendships are crucial. If there's a rift in their relationship, it would deeply affect Hermione. McGonagall, being a perceptive teacher, might then try to mediate and give Hermione advice on how to handle the situation.
Perhaps he's had a falling - out with his friends. In the Slytherin house, there could be a lot of power dynamics and rivalries. If he's been betrayed by someone he thought was a friend, it would be very upsetting.
She might be initially shocked. After all, Draco is usually seen as this tough Slytherin. But then she could feel sympathy. For instance, she might offer him a handkerchief without saying much at first.
One possible reason could be a misunderstanding in the fanfiction. Maybe Ron said something stupid or insensitive, like in the original series where he sometimes had a hard time expressing his feelings properly. This could have deeply hurt Hermione, leading to her crying.
It's appealing because it shows a different side of the characters. We usually see Hermione as strong and in control, so seeing her vulnerable is interesting. And Fred, who is often portrayed as the fun - loving prankster, gets to show his caring side. It also allows for new interactions between two characters who don't have a lot of one - on - one time in the original series.
Perhaps she's being bullied. In the wizarding world, there could be other students who pick on her because she's a 'Mudblood'. This could be really distressing for Hermione, and when Snape finds her crying, he might be conflicted between his general dislike for Gryffindors and his sense of justice.
Perhaps he's feeling guilty about something that happened during one of his quests. Maybe he made a decision that had negative consequences for someone he cares about, and that's weighing on him. It could also be that he's just had a really tough encounter with a powerful enemy and is letting out the pent - up stress and fear through crying.
One great fanfiction with this scenario is 'A Chance Encounter' where Draco stumbles upon Hermione crying in the library. The story beautifully shows how his initial shock turns into concern and how they start to see each other in a new light. It's a really heart - warming read.