It could be their master. Maybe the master has been corrupted by dark forces. He sees the potential in the kunoichi and fears they will become more powerful than him. So, he betrays them to stop their progress.
Alice might be the one. Given her ability to see the future, if she saw something bad happening to Bella but didn't warn her because it would disrupt the Cullens' plans, that would be a major betrayal. She could have known about a danger approaching Bella but chose not to tell her in order to protect the family's interests instead.
In the '4 kunoichi gets betrayed fanfic', it could be that the four kunoichi are working for a noble cause. However, one of their own, due to jealousy of the attention the others get, decides to betray them. She spreads false rumors about them, making the whole ninja community turn against them. The four kunoichi have to prove their innocence and also figure out a way to deal with the traitor within their group.
Another possibility is that it could be a new character introduced in the fanfiction. This new character could be someone who gains Harry's trust quickly but then betrays him for personal gain or because they are secretly working for an enemy. For example, a new student at Hogwarts who seems friendly at first but is actually a spy for a dark wizard.
It could be her best friend. You know, sometimes jealousy can rear its ugly head. If Mikan has something that the friend desires, like popularity or a special talent, the friend might betray her out of envy. For example, the friend could start bad - mouthing Mikan behind her back to gain more attention for themselves.
It could be an enemy who has infiltrated his team disguised as a friend. For example, in a crossover with Fullmetal Alchemist, an alchemist with the ability to change appearance might pretend to be on Kakashi's side but then betray him.
It could be his friend, like Mitsuki. Mitsuki has his own secrets and goals, and in some fanfiction, he might be forced to betray Boruto for the sake of some greater good in his mind. For instance, if he has to choose between following Orochimaru's orders and staying loyal to Boruto.
In some versions, it could be an evil version of one of Tails' friends. Maybe through some dark magic or experiment gone wrong, Sonic or another friend turns against Tails. Their altered state makes them see Tails as an enemy, and they start to undermine him and try to harm him, which would be a huge betrayal for Tails.
Cinder Fall could be a likely betrayer. She's already a villain in the original series, and in a fanfiction, she could pretend to be an ally to one of the RWBY members only to betray them at a crucial moment, perhaps leading them into a trap set by Salem.
It could be a jealous demigod. Maybe someone who is envious of Percy's popularity and Nico's unique powers. This person might see an opportunity to get rid of them and take their place in the demigod hierarchy.
It could be Valerie. She has had a somewhat rocky relationship with Danny in the original series. In a fanfiction about betrayal, she might be pushed over the edge by jealousy or a misunderstanding about Danny's powers and his intentions. She could then use her ghost - hunting skills against Danny in a more malicious way than before.