There could also be a powerful, corrupt magical creature as the antagonist. This creature might have some grudge against humans in general or specifically against Harry and Ginny because of their past actions. It could use its magic to make them disappear and keep them trapped in its domain.
Voldemort could still be the antagonist even if they travel back in time. If they go back to a time when he was already active, like when he was at Hogwarts as Tom Riddle, he could oppose their attempts to change the future or disrupt his plans. He might sense their presence and try to eliminate them.
It could be a rival student from Hogwarts. Maybe someone who is jealous of Hermione and Ginny's friendship or their popularity. This student could try to sabotage their shopping trip by causing trouble in the shops they visit, like making items disappear or spreading false rumors about the things they buy.
One possible plotline could be that they disappear to escape a new dark threat that has emerged in the wizarding world. They might be seeking a powerful magical artifact to defeat this threat and have to go into hiding to find it.
It could be a dark wizard who wants to prevent Ginny from meeting James and Lily. Maybe this wizard has some grudge against the Potter family and knows that if Ginny meets them and learns something important, it will foil his evil plans.
A power - hungry merman who wants to rule over all the mer - people. He sees Harry as a threat because Harry has some special powers or a claim to the throne that he doesn't want to share.
It could be a jealous student. Maybe there's a Gryffindor who is envious of Creevey's friendship with Harry. This student might spread rumors about Creevey, saying that he's only using Harry for his fame. This causes some tension between Harry and Creevey at first, but they eventually figure out the truth and strengthen their bond in the face of this false accusation.
It could be a rogue wizard who has also acquired Muggle weapons and is using them to cause chaos. This wizard might be jealous of Harry's fame and wants to use the gun to prove that he's more powerful.
A new dark wizard who has emerged from the shadows, someone who idolized Voldemort and is trying to pick up where he left off. This antagonist could be using new and more insidious magic that Harry has to figure out how to combat as an Auror.
Voldemort's remaining followers could be the antagonists. Even though Voldemort is gone, there are still some Death Eaters who are bitter about their loss. They might see Harry leaving with Fleur as an opportunity to get revenge on Harry or to use Fleur as a hostage to gain power. They could try to ambush them on their journey, creating a lot of dangerous situations for Harry and Fleur.
A rogue French wizard who has a vendetta against the Delacour family could be an antagonist. He might see Gabrielle as a way to get back at her family and Harry as an obstacle in his path. This wizard could use dark magic and try to manipulate events to his advantage, causing trouble for both Harry and Gabrielle.