One possible reason could be that she broke a school rule in the fanfiction. Maybe she was caught using magic outside of class in a way that was against Hogwarts' regulations.
Perhaps in this fanfiction, Hermione made a mistake that endangered other students. Like she experimented with some powerful and dangerous magic without proper supervision, and Dumbledore had to punish her to set an example and also ensure the safety of everyone at Hogwarts.
In some fanfictions, Dumbledore might get punished for his past mistakes. For example, his actions regarding Tom Riddle when he was at Hogwarts could be seen as negligent in hindsight. He might have missed signs that could have prevented Voldemort's rise, and the wizarding community in the fanfiction could hold him accountable for that.
One possible reason could be that Mirabel might have accidentally broken an important family heirloom. In the context of the Encanto family, their heirlooms are often tied to their magic and family identity. If she damaged something like that, Abuela, who is very protective of the family's traditions and magic, would likely punish her.
One possible reason could be that she discovers some of Dumbledore's past actions that seem morally ambiguous. For example, his handling of the situation with Tom Riddle when he was at Hogwarts. Maybe she finds out some details that make her question his judgment.
Maybe the higher - ups misjudged him. They could have been influenced by false information or just had a pre - conceived bias against Tony. For example, if there was a case where evidence was planted to make it seem like Tony made a mistake, and the superiors didn't bother to dig deeper.
She could be misinformed. For instance, if someone she trusts tells her false things about Dumbledore's past or his intentions. It's also possible that she discovers something about Dumbledore that she believes is unforgivable, like a secret alliance with dark wizards.
She might be very disappointed in herself. Hermione is usually a rule - abiding student, so getting punished by Dumbledore would likely make her feel that she let him down.
One possible reason could be a miscommunication. Maybe some evidence is misinterpreted, and Dumbledore thinks Hermione has broken a major rule. For example, if he thought she was involved in some dangerous magic experiments without permission. But this is a hasty conclusion for him to make.
One possible reason could be a misunderstanding. Maybe there was a miscommunication between Hermione and her friends, which led to them leaving her in the fanfiction. For example, if Hermione made a decision without consulting them, they might feel left out and decide to leave.
In a more extreme case in the fanfiction, Dumbledore might assign Hermione to a special project that is both difficult and dangerous as a form of punishment. For example, he could send her to study a group of cursed magical creatures in the Forbidden Forest. This would be a punishment that not only tests her skills but also her courage.
In some fanfictions, he might be exiled from the wizarding community. This would isolate him from the people and places he cared about, such as Hogwarts and his friends. It would also serve as a public condemnation of his actions.