Capt. Roper is in a gunfight in Death Valley and is shot in the left shoulder. When riding into town his right arm is in a sling.
When Capt. Roper is camping with his troop for the night and hears the noise of Mescaleros chasing a stagecoach the scene goes from night time to bright sunny day to night time again by the time the stagecoach comes to a complete stop (19:07 to 20:18).
Near the end William Holden gets shot in the left arm when challenging the Indians but at the very end of the movie his right arm is bandaged instead.
Director John Sturgess likes to dress his P.O.W officers in their dress uniforms. Common sense would dictate that a soldier is usually not wearing his dress uniform when captured and wouldn't get issued one while in prison.
There were no Union Civil War POW camps in Arizona. In fact the closest one to Arizona would be a Confederate one in Tyler, Texas.
All the Union soldiers were wearing brand new uniforms and boots.
Carla has so many outfits that is stretches credulity.
The ladies' dresses had zippers, which were not invented until 1913.
"Oh Dem Golden Slippers", which is heard in the saloon in Lordsville, was written in 1879;
"De Golden Wedding", which is heard as a theme, was not written and published until 1880.
About 2/3 into the movie Roper walks past a trooper singing the Pete Seeger song "John Brown's Body". The poem itself was written by Stephen Vincent Benet in 1928; the song much later.
The time of the movie was 1863 according to the introduction but the revolver and the carbine used ( Colt Peacemaker in .45 colt and Trapdoor Springfield in .45-70) were not invented until 1873.
Although the film is set in Arizona, when Captain Roper is with Carla Forester in the camp after he rescues her from the stagecoach, towards the beginning of the movie, the matte painting clearly shows Devil's Tower which is located in Wyoming.