I can see the point of wrongly generalizing these stories under a single "Native American" banner, especially when there are people fighting to be recognized individually as separate, unique societies that are still (somehow) alive today.
I'm not versed in the subject, but from studying a bit of trickster folklore in college one can see how different some of them were.
On the other hand, fiction has always traded in direct and off hand references not only to myth, but real events and religions. I don't think she meant to appropriate anything, just color her own universe with a little bit of relatable history like she did before, but again, I can also see how marginalized societies can think of this as "colonialism".
It's a touchy subject, so, I'm not sure how else to react to this. In general, I don't care too much, but I can't blame people for fighting the fights close to their hearts.