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.
Maybe Harry notices some small physical differences. For example, one of them might have a slightly different hair part or a unique freckle pattern.
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.
His friends like Annabeth would surely be main characters. She is smart and resourceful, so she would be leading the search for Percy. Grover could also be a major character. He has a strong sense of loyalty and his connection to nature could be useful in tracking Percy down.
Luke could also be a prominent character. Since he has a complex relationship with Kronos in the original story, in fanfiction he could play a role in either helping or hindering fem Percy's efforts against Kronos. Nico di Angelo is another possibility. His powers over the dead could be useful in a fight against Kronos, and he might team up with fem Percy for that reason.
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.
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.
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.
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.
In the fanfiction, perhaps Harry has a special ability or spell that helps him tell the twins apart. Or it could be as simple as the twins deliberately giving him some secret signs or signals to help him differentiate. Another possibility is that Harry notices differences in their magical auras. Each person's magical aura can be unique, and Harry, being observant, might have detected this difference between the twins.