It's possible that they would accidentally disrupt the timeline in the 'Harry and Teddy go back in time fanfic'. This could lead to all kinds of unforeseen consequences. They might create new threats or change the relationships between different characters in unexpected ways.
It could be alternate versions of the villains from their own universe. For instance, an alternate Voldemort who is even more powerful. Maybe there are also new characters who oppose Harry and Teddy just because they are outsiders in this alternate universe.
In this fanfic, they might encounter alternate versions of themselves. For example, Harry could meet a version of himself who is a dark wizard instead of a hero. Teddy, with his shape - shifting ability, could have a hard time adjusting to the new universe where the rules of magic might be different. They may also find new magical creatures that don't exist in their original universe and have to figure out how to interact with them.
Well, if Harry and Neville go back in time in fanfic, they could use their knowledge from the future to their advantage. Neville might be able to save his parents who were tortured by Bellatrix. Harry could also try to save Sirius earlier. They could also learn more about the secrets of Hogwarts that were lost over time.
It could be a dark wizard from the past who somehow senses that Harry and Teddy don't belong in that time and tries to use their presence for his own evil gains. Maybe he wants to steal their future knowledge to become even more powerful.
One challenge could be the Time - Turner rules. If they are using a Time - Turner, they need to be very careful not to break any of the laws regarding time travel. For example, they can't be seen by their past selves or make significant changes that would disrupt the future they come from. Another challenge is the danger of the time period they visit. If they go to a time when Voldemort was active, they are at great risk of being detected by Death Eaters.
Voldemort could still be a main villain. Imagine if Teddy and Harry travel back in time and Voldemort discovers their presence. He might see them as a threat to his plans and try to eliminate them. This would lead to a lot of dangerous encounters and battles.
A third idea might be that both Harry and Teddy accidentally travel to a time in the past where a great magical event took place, like the founding of Hogwarts. They have to figure out how to get back to their own time while also trying not to disrupt the events that are crucial to the wizarding world's history. They might even learn some long - lost spells or magical knowledge during their time there.