did you pick up the puppy or was it shipped/delivered? did it have the bordetella vaccine? kennel cough is very common in dogs and spreads very easily.. just like any cold we could get.(you may want to keep other dogs away from your pup till this clears up) so, just based on that I wouldn't return the puppy. you may want to call your vet and get more info on the skin infection?! if they said it will go away, I'm sure it will.. but I would definitely want to know what it was exactly and would let the breeder know about the cough and infection. maybe their vet didn't catch it? and the symptoms weren't there for a few days.. in any case I would notify the breeder. I could be wrong but I think sometimes the bordetella vacc. can cause kennel cough.. anyone is free to correct me on this..
good luck, I would keep the pup as long as everything is on the up and up