2 of 2 added links and clarification

Edited to correct my faulty memory,

In the film Harry did see Peter Pettigrew. When Harry was walking down one of the corridors at night he saw Peter coming towards him on the map but he couldn't see anybody because Peter was in his Scabbers form.
Later when Lupin confiscated the map, Harry told him that it didn't work right because it showed Peter Pettigrew who was supposedly dead.

In the book Harry never uses the map when Ron has Scabbers with him. As to why Fred and George never saw him it may be explained with how the map is built.

This video of the Noble Collection Marauders Map shows separate sections of the map that allow you to essentially zoom in on a specific area. You start with a large view of all of Hogwarts and then fold out other parts of the map depending on need. As Fred and George were more intent on either getting out of Hogwarts or hiding from certain people they may not have bothered with looking for where Percy was.

As to the question of the number of people at Hogwarts which keeps popping up as a reason why they never saw him:

BeyondHogwarts lists JK Rowling saying there are around 1,000 students.

HarryPotterLexicon says the books show about 300 with 5 boys and 5 girls added to each house every year.

Another HPLexicon comment has Rowling saying 600 but admitting she is bad at math.