Unless the breeder misrepresented to you what registration she was using for her pups, then I'm not sure there is much you CAN do.
You will not be able to register him or the pups w/ Canadian KC or AKC, unfortunately.
Not all CKC breeders are shady, dishonest puppy millers--there are dishonest breeders in ANY and EVERY registry. But it does sound like you had the unfortunate experience of dealing with someone who cared more about getting a sale than working with you, the new owner.