They were bones from earlier peoples overrun by later tribes who were overrun by the later tribes as has happened throughout history. Now a small handful of the latest tribe survivors thinks the USA owes them a tax free living.
Actually, I heard about this from an archaeologist at work several years ago. As you said, they were older civilizations that were over taken by other societies (tribes), the latest being the Haudenosaune (aka. The Iroquois)... at least until Europeans came along. From what the archaeologist said, we know very little about those earlier societies.
I don't want my country back... I want my country forward!