Thanks dam10n - this part is pretty important - but should be quite easy to understand
If you are looking for someone with indigenous North American ancestry, Mexican groups are sufficient. If anything this will reduce your power to detect, not produce false positives.
Warren has markers that are found in indigenous American populations but not European populations. The fact that the reference population came from South America means that they can only test for those markers that are common to both populations, which could make her indigenous ancestry seem more remote than it actually was.
Given her stated family lore is consistent with her DNA, it's reasonable to accept it rather than a more exotic, and less plausible idea that somehow she has indigenous South American ancestry.
There is every reason for her to have believed her family lore and it seems to be borne out by her DNA. It's silly (or disingenuous) to pretend otherwise.