I would think that it is extremely unlikely that any reputable breeder would allow his/her puppies to be sold in a pet store.
This! A thousand times!
Reputable breeders care about their puppies. They try to place them in good, loving homes. They are almost always willing to take the puppy back, if for some reason the placement doesn't work out. Because these dogs
matter to them. There's no way in heck that they'd stick their puppy in a window and let just any random stranger off the street purchase it.
Also, to all those folks thinking now that they should "rescue" the poor puppy-mill puppy from a pet store... there are a LOT of other dogs also waiting to be saved from shelters and rescue organizations. They need you, too.
If we purchase from a pet store, our money goes directly to - at best! - an unethical breeder. At worst, we're giving our money to a puppy mill. Which means that, in "saving" that one puppy, we've ensured the production of even more puppies exactly like the one we just purchased.
By way of analogy... Suppose you walked into a store and said, "I want to buy that dog!" And the store owner said, "Wonderful! Now, before you can purchase this one, you have to choose one of these other ones over here to be drowned in the Canal. Which one will it be?" Would you pick a puppy for drowning and then walk away with your new dog feeling good that you saved it? Of course you wouldn't! You'd be appalled and you'd refuse to hurt the other puppy. You'd say, "You're crazy! I'm not buying a dog from you!" Well, this is essentially the same thing, except it's happening out of our direct line of sight.
The only way to "save" pet store puppies is to refuse to purchase them, refuse to patronize stores that sell them, and lobby for legislation against them.