I have very little doubt of what she is crossed with, but that is neither here nor there.
I have seen many cases where a breeder (I use the word loosely) owns both the sire and dam. And yes, the breeder believes that the dam mated with the sire, until the puppies are born and it becomes blatently obvious that some other sire got in there (so to speak. )
I honestly think this may have been the case here. Some 'breeders' even have so little knowledge and experience, they can't even tell the difference; others have an inkling but prefer not to accept their suspicions.
As long as you are content with your purchase and your puppy ShadowStaff, there isn't an issue about it for you. However, many ppl out there do have a problem with unethical selling as they spend a good amount of dollars purchasing what they believe is a purebred dog, only to later find out they've inadvertently been duped, unintentionally - or not.