1. Bad Health: Because so many pet store pups come from puppy mills, they are not the result of careful breeding and they are usually not well cared for before coming to the store. Some common illnesses and conditions are neurological problems, eye problems, hip dysplasia, blood disorders and Canine Parvovirus.
2. Behavioral Problems: Because breeding is indiscriminate, behavioral problems are not weeded out generationally. You'll also find that a pet store's staff is not likely to have any training in dealing with behavior issues so the puppies continue to do the wrong things, which become habit.
3. No Socialization: Pet stores pups are often pulled away from their litter at far too young an age, often at only four or five weeks. The earliest a puppy should be separated from his pack is eight weeks and most reputable breeders will say at least 10 weeks. This lack of time socializing with his siblings means that puppy will not develop important canine skills. Likewise, a puppy who has not been handled by people from about three weeks will not naturally socialize well with them.
4. The Downfall of the Standard: In a broad sense, purchasing a puppy from a pet store and then breeding her means you are ruining the standard of that breed because the previous breeders were not concerned with it.
5. Lack of Information: A member of a pet store staff is not an expert on a breed and often not on dogs in general. Purchasing a puppy from a store means you will not get the lowdown on that breed or likely help with any behavioral or other questions.
6. Return at Your Puppy's Peril: Most pet stores do offer a warranty of sorts where you can bring the puppy back if he has problems. They don't tend to tell customers that the puppy's fate, once returned, is usually euthanization.
7. Housebreaking is a Chore: Pet store puppies have spent all their short lives in cages. They do not have the opportunity to develop the natural canine instinct of eliminating away from their food and bed. This causes problems when you try to housebreak them.
8. What You See Isn't Necessarily What You Get: If you see what looks like a Maltese in the window, you may find, as she grows, that there's a little Maltese in there somewhere but mostly she looks like a Terrier. There is no guarantee you will get a purebred dog if that's what you're after.
9. Poor Value: A puppy from a pet store generally costs between $400 and $2,000. This is often more than you'd pay at a reputable breeder who can ensure you get a healthy puppy and provide support afterward.
10. Questionable Pedigree: You're paying for a pedigree, or AKC papers, when you buy a puppy from a pet store but it's very likely that it's not genuine. If the papers are genuine, it still doesn't mean the puppy is a good example of its breed - you need a reputable breeder to prove that.What are our options other than pet store puppies? Reputable breeders are always a good choice. They are very knowledgeable about the breed they represent and can help with behavioral and physical issues that might come up later. These breeders socialize their puppies early on, breed in good traits and breed out bad ones and they can show you your puppies' parents and give you their history.Another great option is adopting a puppy. Humane Societies, local animal shelters and breed rescues are all good places to look. True, you don't have the benefit of meeting you pup's parents but rescued puppies are thoroughly examined for any illness or condition, are socialized by staff and trained early on. Also, if you adopt a mixed puppy you will likely find he is very healthy as mutts are often healthier than purebreds.
From Dogster.com