Another way is through their relationships with other people. Maybe Fred has a closer bond with Lee Jordan and George with someone else. Hermione, being part of their social circle, could use these connections to distinguish between the two. Also, their reactions in different situations might vary. One might be more likely to step forward in a dangerous situation while the other might hold back slightly, and Hermione would notice these subtleties.
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.
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.
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 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.
They might use their humor. For example, if someone is making Hermione feel bad by teasing her about her studious nature, Fred and George will crack jokes at the teaser's expense, making Hermione laugh and feel better, which is a form of protection in a way.
Fred's reaction could be a complex mix of emotions. On one hand, he might be overjoyed at the thought of having a child with Hermione. He may immediately start making plans for their future as a family. However, he could also be a bit worried. After all, having a baby is a big responsibility. But his natural optimism would likely shine through, and he'd assure Hermione that they can handle it together. He might also crack a few jokes to lighten the mood, saying something like 'Our baby will be the most mischievous one in Hogwarts before we know it!'
It could be as simple as their voices. Maybe one has a slightly deeper or higher pitch than the other. Hermione, being intelligent and detail - oriented, pays close attention to these nuances and is thus able to tell them apart.
Often, in these fanfictions, Hermione's intelligence complements the twins' creativity. Her knowledge of magic and books could be used to enhance their pranks or business ideas. Their relationship might develop as they work on various projects together. It could be that they find themselves relying on each other more and more, and feelings start to grow from that mutual trust and respect. The twins might be the first to realize they have deeper feelings for Hermione as they see her in a different light compared to other girls at Hogwarts.
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.
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.