The army supported segregation. It maintained separate facilities where possible. The Buffalo Soldiers built many forts whose facilities at times they couldn't use. At Fort Concho for example, there were separate rooms for educational purposes, etc. The necessities of military life forced white and black troops together, breaking down long standing prejudices. Black soldiers who fought in the Indian Wars, fought their opponents as they have done throughout this country's military history.
Seeing that even when they fought together, side by side, that white soldiers still thought of black soldiers as lesser than, is annoying to say the least. They could not put aside for a moment the melanin count in their skin to realize that they are fighting for the same cause, for the same country, over the same hatred for something. It's ridiculous, and it's still happening today.
Davis, Stanford L. "BUFFALO SOLDIERS & INDIAN WARS." BUFFALO SOLDIERS & INDIAN WARS. N.p., n.d. Web. 5 May 2016.