In many cases, another breed will be mixed into the bloodline. This may seem impossible if a Yorkie is a registered purebred.
However, in looking at the AKC as an example, a three generation pedigree must be established for a dog to be classified as a purebred. This means that there can be another breed mixed in anywhere, 5, 10, or more generations back.
In these cases, there can be a 'throwback' jumping of genes. The Yorkie will have size traits from a very distant relative that was a different breed.
Another possibility is an unintended pairing, though with the AKC, this is being weeded out with DNA testing. DNA testing is voluntary in many cases. However, in some cases it is mandatory. This holds true for frequently used sires (due to their high impact on AKC stud books), for imported dogs, and when done during random inspection visits to breeding kennels.
With this scenario, and without DNA testing, breeders are on the honor system when filling out sire and dam information. Whether there is some dishonestly or
a honest mistake, the sire listed on the registration may indeed not be the actual sire.