What were the longer term more fundamental causes of the inability of whites and indians to avoid such event such as the wounded knee massacre?

The simple answer is the continual expansion of white settlers in a westward manner. The whites found the Indians to be "savage", meaning beneath them in civilization and culture. Early on in America, the term "manifest destiny" was coined with relation to settling America from the Atlantic to the Pacific. As the whites thought the Indians were beneath them, they stopped at nothing, including cruel slaughter and frequent, forced migration to ever more inhospitable lands.