My understanding is that they did not even have any Native American DNA to use for comparison purposes. That they used Central or South American DNA in the hopes that it would approximate.
My great-great-grandmother, Mary Jane Beaver, was 100% Cherokee. My cousin, for whom Mary Jane would have been her great-grandmother, had one of those ancestry DNA tests run. It concluded that she had zero Native American DNA. LOL in spades. My cousins on that side of the family look like they could have walked off the reservation had they grown their hair long.
Matching up people with familial ties using DNA is one thing, determining ethnic and racial history is a much different matter.
Whoa!