When Sergeant Trainor goes to talk to Black Cloud and the other Indian leaders, he passes the body of a dead Indian lying with its head towards the Mission walls. While he is talking to the Indian leaders, some Indian warriors collect this body, which is now lying with its head away from the Mission.
The townswomen in dresses and bonnets during the town massacre are obviously men.
In many scenes in the ruined mission, light reflectors cast the actors' shadows on the walls in 180 degree opposition to shadows elsewhere cast by the sun.
When Rusty is hit with an arrow through the heart near the end of the movie & dies, you can clearly see him breathing.
The last shot shows a hat with a 'crossed sabers' badge, with a '14' above and a 'G' below the sabers. The number represents the number of the cavalry regiment. However, the USA had only 10 cavalry regiments during this period.