J.K. Rowling said they’d be unlikely to recognize the name.
J.K. Rowling addresses this in the F.A.Q. of her old website. She says that Fred and George wouldn’t have been likely to recognize the name Pettigrew as an assumed murder victim, and furthermore would have only been looking at the parts of the map showing where they were planning pranks. That implies they wouldn’t be checking in on their brother’s dormitory frequently.
Why didn't Fred and George notice Peter Pettigrew on the Marauder's Map before ("Prisoner of Azkaban")?
It would not have mattered if they had. Unless somebody was very familiar with the story of Sirius Black (and after all, Sirius was not Mr. and Mrs. Weasley's best friend – indeed, they never knew him until after he escaped from Azkaban), Fred and George would be unlikely to know or remember that Peter Pettigrew was the person Sirius had (supposedly) murdered. Even if Fred and George HAD heard the story at some point, why would they assume that the 'Peter Pettigrew' they occasionally saw moving around the map was, in fact, the man murdered years before?
Fred and George used the map for their own mischief-making, so they concentrated, naturally enough, on those portions of the map where they were planning their next misdeeds. And finally, you must not forget that hundreds of little dots are moving around this map at any given time… Fred and George did not know everyone in school by name, so a single unfamiliar name was unlikely to stand out.
- Why didn't Fred and George notice Peter Pettigrew on the Marauder's Map before ("Prisoner of Azkaban")?, (J.K. Rowling’s website)
Fred and George wouldn’t have recognized the name if they saw it in passing, and wouldn’t have been paying much attention to their brother’s sleeping quarters, so they wouldn’t have realized that there was no Peter Pettigrew in Gryffindor two years below them and gotten suspicious of him.