There could be a group of dark wizards who believe that Harry's daughter has some sort of special power or prophecy associated with her. They want to either use that power for their own evil purposes or prevent her from fulfilling the prophecy, so they become the main antagonists in the fanfiction, constantly plotting against her and her family.
It could be a new dark wizard who wants to use Harry's daughter to get revenge on Harry. This wizard might be jealous of Harry's fame and power and think that by harming his daughter, he can destroy Harry's happiness.
Voldemort or his remaining Death Eaters could be antagonists. They might see her as a threat due to her unique combination of powers. Also, there could be some anti - mutant groups in the wizarding world who oppose her existence.
The main antagonists could be those who envy her wisdom. They might be jealous of the attention she gets or the power that her wisdom gives her. So, they try to undermine her at every turn, spreading false rumors about her or trying to make her look foolish in front of important people.
Sauron, even in the context of this fanfiction crossover, could be an antagonist. His influence could reach the wizarding world through the One Ring. He might try to manipulate Harry or those around him to get the Ring back.
Voldemort could still be a main antagonist. He might be especially interested in Harry's Sacred Gear because it could potentially give Harry an edge over him in their battles.
The Joker would be a classic choice. His chaotic and unpredictable nature would pose a great threat to Batman's daughter. He might try to corrupt her or use her as a pawn in his evil schemes against Batman.
It could be a group of dark wizards who are jealous of Harry's status and see Lemon as a way to get to him. They might try to kidnap her or manipulate her to get Harry to do their bidding.
It could be some of the pure - blood supremacists. They might see her as an abomination because of her connection to Hecate, who is not part of the traditional wizarding families. They would try to undermine her at every turn and make her life difficult at Hogwarts.
The other gods who don't trust Hades might be antagonists. They could see Bella as a threat because of her relation to Hades. For example, Zeus might be worried that Bella could one day try to overthrow him or cause trouble in the order of the gods.
One possible group of antagonists could be those in the Hidden Leaf Village who still hold a grudge against the Kyuubi. They might see the daughter as a threat and try to get rid of her. Another could be rival villages that fear the power she might possess and see her as a weapon that could be used against them in the future, so they would try to eliminate her before she becomes too powerful.
The Ministry of Magic could be the antagonists. Since Harry is in a gang, they might see him as a threat to the order of the wizarding world. They could send Aurors after him and his gang mates, trying to arrest them and break up the gang.