The American Indian Wars lasted from 1776 - 1924. During that time I am aware of at least 4 United States coins featuring an "Indian" on the face:
Three out of four of those were during the waning years of the Indian Wars. The one that really stands out to me is the Indian Head Penny, which was minted during the height of Manifest Destiny.
Why would the United States celebrate people who were enemy combatants at the time of the minting? (Obviously I know not all Native Nations were enemies at all times, but I assume the US Mint didn't have the most progressive and nuanced thoughts on the indigenous population of the North American continent.)
(Thanks to /u/CashMaster76 who put this question in my head on a post in /r/coins.)