The Hogwarts faculty could also be antagonists in a way. Some of the more traditional and strict professors might not like Hermione's distraction with the Chocolate Frog Card. They could try to confiscate the card or give her detention every time she tries to pursue the mystery behind it. This would create conflict as Hermione has to find ways to outwit the professors while still trying to solve the mystery of the card.
A dark wizard from the past whose secrets are being unearthed because of Hermione's exploration of the Chocolate Frog Card could be the main antagonist. Maybe the wizard was banished long ago and doesn't want his secrets revealed. He could start to influence events at Hogwarts through dark magic, trying to stop Hermione from learning more about him. For example, he could possess other students or create dangerous obstacles in Hermione's path.
It could be a Muggle - born witch who discovers the magic of Chocolate Frogs. She might use her unique perspective as a Muggle - born to solve problems related to the Chocolate Frogs that the wizard - born characters overlook.
One idea could be that Hermione discovers a rare Chocolate Frog Card that has a prophecy on it related to her future at Hogwarts. This could lead her on a quest to figure out what the prophecy means and how it will impact her friendships and studies.
Maybe the main antagonist is a jealous rival. This rival is envious of her abilities and status, so she uses a forbidden magic to turn her into a card. The rival then tries to take her place in the story, but her friends start to suspect something is wrong and begin to investigate.
A group of Death Eater sympathizers within the Ministry could be the main antagonists. They still hold onto the old pure - blood supremacist ideals and see Hermione, a Muggle - born witch, as a threat. So they fabricate evidence against her and send her to Azkaban to send a message to all Muggle - borns that they are not welcome in the new wizarding order they are trying to create.
It could be that Ron's own insecurities and pride are personified as an antagonist. His jealousy towards Hermione's achievements and friendships could be like a dark cloud over him. Severus has to save Hermione from this negative side of Ron. So in this case, Ron's inner demons are the antagonists that Severus must combat.
It could be a rogue wizard who has a grudge against Hogwarts. He might be using dark magic to create disturbing situations for Hermione and Hagrid to deal with. For example, he could be making the magical creatures in Hagrid's care go wild or messing with Hermione's study time by causing strange noises and apparitions in the library.
Perhaps an ancient evil force that has been trapped in the Sorting Hat for centuries and is trying to use Hermione as a means to break free. The force could start influencing Hermione's thoughts and actions in a negative way, and she has to fight against it with the help of her friends and the positive magic of Hogwarts.
Another possibility is a dark wizard or a group of dark wizards who are after some powerful magic that the Lestrange family has, and Hermione gets in their way as she tries to protect the family or uncover the secrets. They would be the main force that Hermione has to face and overcome throughout the fanfiction.
Perhaps a powerful magical being from a different realm is the antagonist. This being might mistake Hermione for someone else or see her as a key to something in the wizarding world. So, it uses its magic to make her disappear. This being would be very difficult to defeat or negotiate with, making it a huge challenge for those trying to find Hermione.
Maybe a new dark wizard or witch emerges. This character is extremely powerful and manipulative. They target Ron and Hermione because they are Harry's closest friends. By turning them against Harry, this antagonist hopes to isolate Harry and make him easier to defeat. The new antagonist could have some unique magical abilities that allow them to control the minds of others or create very convincing false scenarios.