Bellatrix Lestrange could also be a common antagonist. She was extremely loyal to Voldemort and very powerful. If Harry and Hermione's actions in the past disrupt the Death Eaters' plans, she would surely oppose them.
There could be time - traveling dark wizards who oppose Harry and Hermione's attempts to fix things in the past. These wizards might have their own agendas for the past and present, and see Harry and Hermione as threats to their plans. They could use dark magic to try and stop them or even manipulate time against them.
There could also be new dark wizards or witches who envy the power and fame that Harry and Hermione have. They might see the child as a way to get to Harry and Hermione, or they might simply want to prove themselves by challenging the family. For example, a dark wizard who has developed a new and dangerous form of dark magic and wants to test it on the child.
Often, it could be dark wizards from the past who oppose Harry and Amelia's attempts to change things for the better. For instance, a dark wizard who wants to keep a certain evil spell in place that Harry and Amelia are trying to stop.
It might also be time itself. There could be some sort of time - related magic or force that doesn't want the past to be changed. So Harry and Tonks would have to face this 'antagonist' as they try to rewrite history. This could be in the form of time - locked spells or magical barriers that prevent them from interfering in certain events.
In some cases, time itself or the consequences of changing time could be seen as an antagonist. For example, if they try to change a major event, they might face unforeseen consequences like creating new threats or endangering the future they came from. So, in a sense, the very fabric of time and its rules could be working against them.
Danzo Shimura might be another one. He is very secretive and power - hungry. If Naruto and Naruko's time - traveling actions expose his dark deeds or interfere with his control over the village, he would become their enemy. He has many underhanded methods and a strong influence within the village that they would have to deal with.
One possible main antagonist could be a dark wizard from the past who senses Hermione's interference in the timeline and tries to stop her. This wizard might be afraid that Hermione's actions will change history in a way that will end his power or influence.
Danzo could also be a common antagonist. He was very power - hungry and had his own dark secrets. In a time - travel scenario, he might view Kakashi and Naruto as threats to his control over the Hidden Leaf Village in the past. He could try to eliminate them to maintain his grip on power.
It could be a group of dark wizards who have escaped from Azkaban and formed a new dark alliance. They might be seeking revenge on Harry and Hermione for their role in defeating Voldemort.
Often, the goblins can be antagonists. If they have their own motives that conflict with Harry and Hermione's, like protecting a dark secret in the vaults or trying to take advantage of the situation for their own gain. Another possible antagonist could be a Death Eater who has infiltrated Gringotts to either steal something important or to ambush Harry and Hermione.