Ever since someone on tumblr pointed out that it doesn’t make any sense that Peter lives with Ron for three years, yet Fred and George fail to notice this on the Marauder’s Map, I’ve been wondering how this can be explained. I finally figured it out!
It’s because the Map shows names of Animagi only when they’re in human form, and, when they are in animal form, only if the Map’s user knows that they are Animagi. Think about it: nobody except Lupin, who had witnessed their transformations countless times, was able to see Peter and Sirius in animal form on the Map. Snape only saw Lupin and Sirius in the Shrieking Shack (who were both in human form), but not Peter (who was a rat at the time). Harry also never saw Rita Skeeter on the Map when she was a beetle.
I’m pretty sure the Marauders included this feature because should the Map ever be found by a teacher, their being Animagi would still remain a secret. This would’ve been more important to them than the Map being completely accurate. Lupin didn’t even tell Dumbledore Sirius could turn into an animal when he thought Harry’s life was in danger. That’s how much he wanted to keep it a secret, even over twelve years later.
EDIT: Several people told me that Harry sees Peter’s name on the Marauder’s Map in the film. This is because the production staff never cared about things like logic or continuity, and least of all about what actually happened in the books.