not all pet stores get dogs from puppy stores
Anyone who breeds for the purpose of selling to petstores is a puppy mill. It doesn't matter how clean or well-taken care of the pups or parents are..if the pups are in a petshop, they are from a puppy mill (with the exception of people giving them accidental litters). A paper mill supplies paper. A puppy mill supplies puppies. Even if the pups' parents are registered, health certified, champions, with outstanding pedigrees, and the petstore was only given one litter a year. In my opinion it doesn't matter -- those pups are in a petshop, so they automatically come from a puppy mill.

Obviously it's difficult to check the backgrounds of wthe puppies and where they came from (breeders usually remain anonymous, for obvious reasons), so it's best to stay away from pet store puppies altogether. I really wish they would make it illegal to sell puppies and kittens.