The hunters could be antagonists. They might see the werewolf boy as a dangerous creature and try to hunt him down.
The Ministry of Magic could be a main antagonist. They have a history of being discriminatory towards werewolves. They might see Harry as a threat now that he's a werewolf and try to lock him up or restrict his movements. For example, they could pass new laws specifically targeting him, like making it illegal for him to attend Hogwarts as a werewolf.
I don't know the exact details of this novel, but it could be other werewolves who oppose Dimitri's relationship with Madeline. Maybe they think it goes against the pack's traditions.
It could be other werewolf packs that see Lyla and Derek as a threat to their territory or power. Maybe they want to eliminate them to maintain their dominance in the werewolf world.
It could be other students at Hogwarts who sense something strange about Snape and his invisible friend. They might try to expose Snape's secret out of jealousy or because they think it's some sort of dark magic.
A new and original antagonist could be a rogue psychologist who has developed a powerful hypnosis technique. This character might be jealous of Peter's abilities and want to use hypnosis to take over his mind and use his powers for their own gain. Or it could be a secret organization that wants to use Peter as a weapon, and they use hypnosis as a means of control.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
The father of the baby could potentially be an antagonist if he has a different view on the pregnancy than Lucy. For example, if he wants her to have an abortion and she wants to keep the baby, he could create obstacles for her.
Perhaps there is an ancient evil entity that feeds on the hatred between werewolves and vampires. It doesn't want Sasuke and Sakura to succeed in bringing peace. So it uses its dark magic to create misunderstandings and conflicts between the two, trying to keep them at odds and prevent any chance of unity.
One popular character could be the girl who befriends the werewolf boy. She often serves as the connection between the werewolf boy and the human world. Another might be the werewolf boy's mentor or an older werewolf who teaches him about his heritage. And sometimes, there's a villain, like a hunter who is after the werewolf boy, which adds conflict to the story.
It's possible that some of the more traditional and strict gods could be antagonists. They might view Aphrodite's act of adopting a mortal boy as going against the natural order. These gods could try to separate the boy from Aphrodite, either by tricking the boy or by putting pressure on Aphrodite. There could also be a dark force or a cursed entity in the story that targets the boy because of his connection to Aphrodite, seeing him as a way to get back at the goddess of love.