Fred and George come into possession of the Marauder's Map in their first year when they steal it from Filch's office. At this point, Peter Pettigrew is Percy's pet until he is given to Ron for his first year, two years later.
This gives Fred and George two full years to notice that an extra boy called Peter is sleeping in their older brother's room/bed at night. Given their propensity to prank Percy, and Percy's attempts to be an authority figure over them, I think it would be reasonable to assume that in two years they would have at least looked for him once at night on the Marauder's Map.
Even if they noticed this, thought it was strange but didn't report it, they then have a further two years of Pettigrew belonging to Ron. Even as a pair of teenage pranksters, I'm pretty sure seeing a man you've seen in your older brother's bed, sleeping in your 11-year old little brother's bed is going to set off alarm bells.
This is assuming they don't just immediately recognize Peter Pettigrew's name when they first see it. Harry Potter's story is well known by everyone in the Wizarding World, as McGonagall says, "There won't be a child in our world that doesn't know his name."
Peter is a hero of the Harry Potter story up until he is revealed as a traitor. He gave his life chasing down and confronting the betrayer of Harry's parents. I should imagine his name would also be well known to Fred and George, as they will have heard the story enough times.
Why don't Fred and George say anything?