It could be Morgana. She has been known to be an antagonist and has a vendetta against Camelot and those associated with it. Poisoning Merlin would be a way to weaken Arthur's most powerful ally.
It could be a jealous classmate. Maybe someone who is envious of Hermione's intelligence and always being at the top of the class.
Perhaps an enemy from a rival group. They might see Sakura as a threat to their plans, so they poison her to get her out of the way. Another possibility is a character who has been secretly harboring a grudge against her for a long time, and finally decides to take action by poisoning her.
It could be Draco Malfoy. He has had a long - standing rivalry with Harry. Maybe in this fanfic, he finally decides to take extreme measures out of envy or pressure from his family.
Well, one possibility is that Merlin's friends, like Arthur, might search desperately for a cure. They could go on a dangerous quest to find a rare herb or consult a powerful sorcerer who might know how to save him. Another could be that Merlin, while poisoned, has strange visions or dreams that give him clues about his true destiny or the future of Camelot.
It could be Orochimaru. He's always been interested in obtaining powerful bodies for his experiments. Naruto's body, with the Nine - Tails' power, would be a great target for him.
It could be a jealous student. Maybe someone who has a crush on the same person Harry is attracted to in the story. They see Harry as a rival and figure that by poisoning him with a love potion, they can make him look foolish or get him into trouble.
Perhaps some of the snooty nobles who look down on Merlin and constantly try to get him into trouble. They could be making fun of his clumsy ways one too many times and he just snaps and hits them with a shoe. It would be a moment of satisfaction for the readers who don't like those arrogant characters.
It could be a disgruntled house - elf. Maybe one that was mistreated by its wizarding family and decided to steal money as revenge. They could use their magic to get into places unnoticed and take the money.
It could be an old enemy of the Hyuga clan. Since Hinata is a part of the Hyuga, someone with a vendetta against the clan might target her.
I'm not entirely sure specifically what'merlin poisoned fanfiction' refers to without more context. It could potentially be fanfiction in which Merlin, from the Merlin legend or related media, is poisoned in the plot of the fictional story created by fans.