The story takes place during the French intervention in Mexico from 1861 to 1867. Dynamite was invented in 1867 by Nobel, yet it was not easily available in the US until at least 1868. A common error in westerns.
The story takes place during the French intervention in Mexico from 1861 to 1867. Hogan is using a Colt Peacemaker pistol, which did not come into use until 1873. The rifles Winchester 1873, Gras 1874, Bertie 1907, and a revolver Colt New Service 1917 were not in use at the movie epoch.
Not only the Colt 1873, but also rest of the small firearms in the movie - rifles as Bertie 1907, Winchester 1873 and Gras 1974 and a revolver Colt New Service - are anachronistic to the story plot, taking place in the 1860s (the French intervention in Mexico).
In a brief scene, when Hogan and the guerrillas enter a church, there is a view of the cloister and altar from above, possibly the choir veranda. The movable altar is seen between the main altar and the benches, but that sort of altar was not in use before 1965, when christian communities installed that so that the priest could celebrate the Mass looking at the people.
Hogan becomes very agitated when he sees Sara wasting water, as if he thinks it's scarce. But minutes later, they travel down a flowing stream. So even if a frontiersman/soldier/mercenary like Hogan couldn't detect that much water so close by, his horses certainly could, and he'd notice their behavior. So he had to know there was plenty of water nearby.
When the first French column is tracking Sara & Hogan in the stream, several French soldiers can be seen staring intently into the stream bed as if looking for signs of the horses they're following. But these men are FAR back in the column, so the bed is already muddy & churned from the preceding soldiers, making it impossible for them to see anything useful.
During the battle for the French Headquarters, Hogan lights and throws a stick of dynamite with power and accuracy using his left hand, when a couple of days before his left shoulder was pierced by an arrow. (He throws other sticks with his right hand after that.)
When "Sister" Sara is climbing the train trestle there is a closeup of her boots slipping on the bracing. The next shot shows a view upward from underneath her and her boots are now black sneaker type shoes.
The train trestle that is "blown up" is an open deck trestle that would be fully supported by the stone towers or "bents". The wooden bracing that Sara climbs would not be needed or serve any purpose other than to give her a way to climb.
When "Sister" Sara is explaining to Hogan the things the three Americans did to her, she motions with her arm, and her underarms are shaven. This couldn't have happened to a woman "in the middle of nowhere" who hasn't been in an area where she could have shaved for a long time.
In the train trestle scene, in the moments prior to the dynamite explosion and resulting crash of the train, there are no wires/cables visible above the trestle. But when the train is seen approaching, wires or cables are clearly visible overhead.
While Hogan and Sara are supposed to make love in the tub, the camera shows Hogan's hat. We can clearly see on the hat the shadows of the actor's hands who are spilling water out of the tub to make it appear as if they were making love.
Despite spending several days in what is a very intense sun, neither Sister Sara's face nor her hands (which are exposed) show any sign of reddening, tanning or burning. Given how fair she clearly is, this should not have been possible.
The goof item below may give away important plot points.
Sara tells Hogan she kept up her charade as a nun because he said he'd be more lenient with her. However, she had the habit before she even met him, and it is never explained how or why she acquired it in the first place.