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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.

I'll edit this when I can find the book to give the exact passage.