The film states that there were 40,000 Apache warriors at war in Arizona, when in fact there were never anywhere near 40,000 Apaches in the entire state and never more than several hundred fighting the white settlers and the US Army at any one time.
The Apaches are shown wearing feathered warbonnets. This was a headdress worn by Plains Indians - which the Apaches weren't - such as the Sioux and Kiowa. Apaches usually wore simple headbands or no headdress at all, but they never wore feathered warbonnets.
Uniforms of the U.S. Cavalry are set during the wrong era. Uniforms shown are from 1870s and the movie is set in 1853.
The beginning of the film depicts the Apaches and Comanches as allies against the Mexicans. In actuality, they were mortal enemies going back several hundred years. The Apaches and other Native American groups had been driven by the Comanches into the hostile desert of the Southwest back in the 17th Century.
Although the film is set in 1853, the Apaches are shown firing repeating rifles that weren't introduced until 1894.
The film is set in 1853, yet Tucson resembles an Old West Town from the 1870's and 1880's both in the type of buildings and the attire of the townspeople.