The framing of the house being built appears to modern construction, using modern lumber, not the rough cut lumber of the day. It also appears to be double wall construction, not the single wall type of the era.
When Everett and Virgil are agreeing to protect Appaloosa, the lighting in the room changes drastically between close-ups and wide shots. For the close-up of Abner Raines, the curtain is open, lighting his face with sunlight, but in the wide shot the curtain is closed.
During the opening murder scene, the cocking lever of the Winchester is fully down (probably a jammed blank didn't eject). There's a cutaway and then while Bragg is still walking away, we clearly see the rifle with the cocking lever is now fully retracted.
When Virgil and Everett first approach Bragg's men in the saloon, the cowboys are relieving themselves at the bar's "piss trough." Virgil demands that they "button up." After the shooting is over, when the bodies are shown on the floor, there is no trough or any sign of wetness in that area.
When Alison and Virgil are in the coffee shop, she orders a coffee and a biscuit. Although refused a biscuit at first until Virgil intervenes, she is actually served a soup and bread roll, which moves around as the scene unfolds. Everett also receives a coffee at the same time, though no coffee has been ordered for him.
When Joe Whitfield approaches Virgil Cole and Everett Hitch the first time in the hotel dining room - shortly into their conversation you can see the numbers "191" flash momentarily in the upper right hand corner.