One interesting plot point could be that Hermione's ability to tell them apart gives her an advantage in a prank war. Since she can identify which twin is which, she can outwit them and turn their own pranks against them. This could lead to a lot of humorous situations and a shift in the power dynamic among the three of them.
Perhaps Hermione's skill in differentiating Fred and George becomes crucial in solving a mystery at Hogwarts. The twins are involved in some way, and her ability to tell them apart helps her figure out who did what and why. This could involve secrets in the castle, hidden passages, or something related to a magical artifact.
It could also be that Hermione's ability creates some jealousy among the twins. One of them might feel that she favors the other because she can so easily tell them apart. This could lead to some tension and character development as they work through their feelings, and Hermione has to navigate the situation to keep their friendship intact.
Another plot point might be that the twins are actually quite amazed that Harry can tell them apart. This could lead to a closer bond between Harry and the twins, and they start to involve him more in their secret schemes because they trust him with this special knowledge.
Maybe she notices their different mannerisms. For example, George might be a bit more reserved while Fred is more outgoing. Hermione is very observant, so she could pick up on small details like how they talk, their facial expressions when they're joking or serious.
In some fanfictions, an interesting plot point might be that Fred and George form a sort of 'protection squad' for Harry. They recruit other students who also care about Harry and together they create a network of protection around him. This could lead to some really exciting adventures as they try to outwit the Death Eaters or other enemies. Another aspect could be that they help Harry with his studies in a very unorthodox way, using their own brand of magic and knowledge that the professors might not approve of, but which is effective for Harry.
One reason could be that they played a particularly mischievous prank on her that went too far. For example, if they made her late for an important exam or meeting with a professor by using one of their wild magical inventions. Hermione, being a stickler for rules and academic achievement, might lose her temper and hex them in retaliation.
One common plotline is them teaming up to play pranks on other students in Hogwarts in a more elaborate and creative way. Since Hermione is very intelligent and Fred and George are creative with their pranks, they combine their skills.
Maybe Harry notices some small physical differences. For example, one of them might have a slightly different hair part or a unique freckle pattern.
It could be that Percy pays attention to their individual interests within the fanfiction. If one of them has a particular hobby or passion that the other doesn't share as strongly, that could be a clue for Percy. Also, perhaps their interactions with other characters differ slightly. Fred might be more likely to tease a certain character, while George has a different way of relating to that same character.
It could show that Percy is more perceptive than the others think. Often in stories, Percy is seen as a bit of a stickler, but this ability to tell the twins apart might indicate he has a deeper understanding of people.
In some fanfics, Harry might be able to tell Fred and George apart by their different interests within the story. For example, Fred could be more interested in potion - making experiments that are a bit on the wild side, while George is more into the business side of their joke shop plans. So when they talk about their hobbies or future plans, Harry can distinguish between them. Also, their sense of humor might be slightly different. Fred might crack a certain type of joke more often, like those related to magical creatures in a really absurd way, while George prefers jokes about Hogwarts professors. Through these nuances in their personalities, Harry is able to tell them apart.
One possible way is through their body language. For instance, Fred might stand with his left foot forward more often, while George has a habit of leaning to the right when he's standing still. Harry, being observant, picks up on these little quirks.