Well, a few things. First, most of us operate under the presumption that half-wizarding, half-Muggle children are going to be wizards and witches. It's quite possible that the children of a witch and a Muggle (e.g.) would have fifty-fifty chances of inheriting magic, or only twenty five percent chance of inheriting magic, if the genes work recessively.
To explain what I mean, though, I was thinking that Native Americans probably did not always distinguish properly between wizards and Muggles - i.e. they sometimes attributed magical powers to Muggles, and sometimes did not notice that wizards had special powers. Given that, it seems highly unlikely that Indian wizards would have worried about "maintaining pure blood lines" or any of that, and if wizards are really so rare, Indian wizards probably married Muggles nearly every time. So why wouldn't there be huge numbers of half-blood Indian wizards (which I suppose arguably there might have been, but it doesn't seem plausible if HP canon includes the basic points of our own history)?