The Indians that attacked the travelers were called Apache. There were no Apache Indians any where near the Missouri area where the film was supposed to be.
At what is believed to be the end of the Civil War, a woman on the train sings "How Great Thou Art", which wasn't written until 1885, 20 years after the Civil War ended.
Electrical outdoor light over the double door building.
The black soldier is shown using a Colt Single Action Army during a gunfight with natives. The Colt SAA was developed in 1872 and adopted by US Army in 1873, well after the end of the Civil War.
Black soldiers (known as Colored Troops) did not generally mix with white troops during battle. If a Black soldier was captured, he would not be made prisoner of war, he'd be sent south in chains as a slave. He certainly would not share a cell (or a room in a house, as seen in the film) with a white prisoner. The officer would have been kept separate.
The locomotive used for the train was actually an oil-fired Baldwin built in 1911. The cars are labeled as D&SNG which was started in 1980. The yard even has a passenger gondola for tourists.
Around the end of the film, when they attack the native camp and one of them grabs one girl and runs away with her, you can clearly see a train bridge made of modern metal trusses - specific to the 60s, in a place where it shouldn't be.
Independence Missouri, is depicted as high plains scrub with visible mountains in the distance.. In reality it is quite near the Missouri River, and 500 miles from any mountains of size. The Virginia POW camp and the family home also look to be in high plains scrub land.