It might be due to a political conspiracy. There could be a group within the Ministry of Magic that wants to get rid of those who oppose their new, perhaps unjust, policies. Ron and Hermione, being known for their strong moral compasses, might be seen as threats and banished as a result.
One possible reason could be that they are wrongly accused of a serious crime within the wizarding world. Maybe some dark magic items are found in their possession and the authorities suspect them of being involved with dark wizards, without fully investigating the real source of those items.
Perhaps a powerful and malevolent magical being has framed them. This being could have the power to manipulate evidence and influence the minds of the wizarding community. So, Ron and Hermione are banished because everyone believes the false scenario created by this entity.
It could be that they lied to Harry about something really significant. In the wizarding world, trust is built on truth - telling. If they told a big lie, like about the true nature of a magical object that was putting Harry in danger, he would be very angry. And if their actions led to the death of someone Harry cared about. For instance, if they made a wrong move during a fight that caused an ally to die, Harry would find it very hard to forgive them.
In the fanfic, Hermione might regret choosing Ron over Harry because Harry has a different level of understanding when it comes to her academic pursuits. Harry, having faced the challenges of fighting Voldemort from a young age, might have a deeper respect for Hermione's thirst for knowledge and her need to constantly learn and improve. Ron, on the other hand, sometimes showed impatience with Hermione's studious nature.
It could be due to a misunderstanding. Suppose Ron overhears a conversation between Harry and Hermione that he misinterprets completely. He might think they are plotting against him or don't really consider him a true friend. So in a fit of anger and hurt, he decides to betray them.
It could be a misunderstanding. For example, Ron might think Harry did something really bad to Hermione or their other friends. Without proper communication, his anger could lead him to punch Harry. Also, if there was some sort of magical influence or dark magic at play that affected Ron's judgment, that could be a reason too.
He would probably become more determined to clear their names. Harry has always been loyal to his friends, so he might start his own investigation, even if it means going against the wizarding authorities.
Well, it could be related to Ron's insecurities. He might be insecure about his place in the group with Harry and Hermione. Hermione is always so confident and sure of herself, and Ron might feel that he doesn't measure up. This could translate into aggression as a way of lashing out. Also, perhaps there's some external influence, like a dark magic object that's affecting Ron's mood and behavior towards Hermione.
One reason could be envy. Hermione is often very good at academics and magic, and Harry and Ron might be envious of her success. For instance, if Hermione always gets top grades in potions class while Harry and Ron struggle, they could lash out at her out of frustration.
One reason could be jealousy. Maybe Ron feels that Harry is getting too close to Hermione and he's afraid of losing her attention. In fanfiction, authors often play with the characters' emotions. Harry, on the other hand, might see Ron as being too possessive of Hermione.
She could be banished due to her unorthodox powers. In many fictional settings, if a character has powers that are different or not understood by the majority, they are often feared. If female Percy has some unique abilities that are considered dangerous or abnormal, the authorities or those in charge might decide to banish her to keep the peace or protect their own interests.
One possible reason could be a miscommunication. Maybe Hermione accidentally reveals a secret of Harry's that he didn't want known, and this causes him to feel betrayed and start to hate her. Another reason could be jealousy. If Hermione gets more attention or praise for her magical abilities than Harry in the fanfic, he might develop feelings of envy and hatred. Or perhaps there's a love triangle situation where Hermione is involved with someone Harry doesn't like, and that causes his hatred.