You found the breeder through a puppy sale/auction site – This may or may not be a red flag. There are people that troll the internet for breeder sites and link them without asking permission. There are sites that contact breeders after a link has been put up and then are slow in taking it down when requested (provided the breeder does not delete the email as spam). However, some breeders intentionally seek out these sites as ways to unload animals. You have to add up various factors. The breeder may not even know someone unethical has added his or her website.
No indication of what the breeder is doing with their dogs – Does the breeder have lists of titles their dogs have won? Remember, a good breeder is trying to better their dogs and the breed as a whole. You cannot do that without being able to prove your dogs are able to perform/work/show successfully. It is not hard to search to find out if a dog has actually won titles either. If in doubt a small internet search for the dog's registered name can help.
Registered exclusively with XYZ – In the United States, you want to look for dogs registered with the American Kennel Club, United Kennel Club, Canadian Kennel Club or American Rare Breed Association. Though no registry is perfect and even the lowest breeder can register if they make the minimum requirements, there have been a glut of less than ethical registries cropping up to cater to those who do not want to meet the requirements, who have lost privileges with other registries, puppy millers, etc. Make certain if you see just letters, that you verify the registry. Some less than ethical ones have used names with the same initials as other registries. Is that A in AKC for American or is it Arthur's Kennel Club?
It is easy to be blinded by flashy sites, claims, cute faces, etc. The internet has made it very easy for unscrupulous breeders to lure the unsuspecting buyer in. If you choose the breeder route over rescue, do all you can to ensure the breeder you choose is not in it for just the money.
Please remember; always consider the rescue option when looking for a companion. With too many owners willing to give up a dog as opposed to working through issues, there will always be dogs in need of new homes. Source: What is in a website?