You really should just stay away from pet stores when buying a puppy. Be especially worried if those puppies are coming from out-of-state, particularly Midwest states (Missouri and Illinois are two of the biggest).
If the breeder cannot let you meet the parents, you should walk away. Not meeting the parents is like buying a car without knowing the make. Don’t do it. For all you know, these people did not even breed the puppy, but are selling him secondhand for unknown reasons.
If you call a breeder and they say “let’s meet somewhere” when you ask to visit their kennel, it’s a puppy mill. Usually they will try to get you to meet in a store parking lot or a park. Unless there are extreme circumstances, there is no reason why should not see where your puppy was born.
Reputable breeders focus on one breed, maybe two, MAX. If you find a site offering five different breeds (and their mixes!), it’s a puppy mill.
When you call the breeder and ask if they have puppies, do they respond with “I have one litter coming, but there is already a waiting list” or “oh yes, I have 5 litters on the ground and 3 more on the way”? If the breeder has 30 puppies, that is definitely a puppy mill.
Dr. Kathryn Primm DVM, owner and chief veterinarian of Applebrook Animal Hospital, says to be wary about the breeder promising a certain size, temperament, or characteristic that seems extreme. For example, a dog came into her clinic that was supposed to be a Pomeranian and Husky mix that the breeder had promised would never grow lover than 7 pounds. She was 42 pounds.
This goes for the dog and the breeder’s home or kennel. Dr. Primm says puppies from puppy mills are more likely to smell like a kennel and have poor coat quality.
Your breeder should care enough about what happens to the puppy that she has a contract protecting both you and her. Reputable breeders have a spay/neuter agreement, breed papers, health contract, and a request that you return the dog to them if it doesn’t work out (rather than dumping him at the shelter).
Another way they can cut their costs is by giving you the puppy early, because they do not have to feed them, give them shots, etc. Question any breeder wanting to give you the puppy before they are eight weeks old. This is the minimum age you should be taking a puppy from their mother and litter-mates.
To sum everything up, A puppy mill cares only about money. They will breed as much as they possibly can to maximize profits. They often breed multiple breeds. Generally they sell to pet stores, puppy brokers, online pet stores fronting as reputable breeders (a reputable breeder would never do that).
A reputable breeder generally has a single breed. They know (and can provide paperwork and evidence) of the pedigree of each puppy going back several generations at least. They do health and genetic testing, have the puppy's parents on site for you to see and can identify each puppy by name. A good breeder will breed 2-3 times per year at most and will generally belong to a breeder club or association. But the bottom line is that it's pretty hard to identify a reputable breeder, so be sure to educate yourself and thoroughly research before purchasing a puppy.