do you have them in with any other species of puffer? a lot of people like to combine dwarf puffers with other fish, but that generally just doesn't pan. dwarves are notorious biters, so if the two species are combined, that might be the problem.
also, what size tank do you have them in? if you have too many puffers for the space available, they very easily could be acting out of stress. try separating out the one with no bitemarks and see if that helps. if it does, build him a new tank or pawn him off on someone else who can keep him on his lonesome. once a biter, always a biter...