In all of the Indian wars, there were some Indians fighting on the side of the US Army (against their traditional enemies).
Northern Plains...
Allies of the US...Shoshone, Ute, Ree, Pawnee, Bannock, Nez Pierce, Crow, Osage, Kaw, Winnebagos, and many smaller tribes such as the Poncas, Otoes, Peorias, Omahs, Mandans.
Southern Plains..
Allies of the US ...
Caddos, Anadarkos, Wacos, Tawakonis, Tonkawas and many more smaller tribes.
We did have a few fights with our allies from time to time. The Nez Pierce and Utes comes to mind.