In the scene near the end at Cantrill's camp, Joe Sawyer is very clearly clean-shaven. But in the Raiders' ride to Lawrence, which takes place that night, he has several weeks' growth of beard.
When Fletch confronts Seton after Mr. McCloud is shot, he doesn't look Seton in the eye.
Throughout the film, Colt Single Action Army revolvers (commonly known as Peacemakers) are used by various actors including John Wayne, Roy Rogers, and George 'Gabby' Hayes. This revolver was not produced until the 1870s. The film is set in the late 1850s and 1860s. The Colt is the 1873 model so it could not have been in the Civil War.
Early in the picture, Franklin Pierce is president (1853-1857) and Kansas is not yet a state (admitted 1861). Angus McCloud announces he is going to Dodge City. Dodge City was founded in 1872.
Cantrell sends a letter to Mary McCloud, telling her exactly where his campsite is. No military leader would send such detail in a letter that could be intercepted by his enemies.