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.
After Hogan's first shot at the dynamite under the trestle, the camera angle reverses to Sara, who takes the rifle, cocks it, hands it back to Hogan, and then re-sets it on her shoulder. When the camera returns to the trestle, the train hasn't moved.
When Hogan takes his last sip of whiskey before the arrow removal, he puts the bottle to his lips. In the next shot, he is already setting it on the ground.
When Sara and Hogan are hiding from the French soldiers in the abandoned building, Hogan's cheroot changes length inconsistently between shots.
Rattlesnakes shake their tails at up to 90 hz (faster than hummingbirds flap their wings). A person could not produce the characteristic warning sound by manually shaking a dead snake's tail.
When Hogan gets shot by the Yaqui arrow the arrowhead is clearly shown sticking out of his back, then a minute later the next shot of Hogan's back shows that the arrow did not fully penetrate.
In the French HQ, when Hogan and Sara ask General LeClaire for champagne or cognac, he relays the order to his subordinate in English and not in French.
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, unless it is falsework left over from construction of the trestle, or unless it was deemed necessary during construction due to some flaw in the supporting structure of the open deck.
At about minute 14-15, Hogan returns from lookout, and scrambles down a hill toward a small stream. Visible through the trees at the top of the screen is a modern highway railing.
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.
When Beltran wakes Hogan in the cave, the Juarista sitting woodenly upright in the background wearing a sombrero is clearly a mannequin. It never moves, and its hands are positioned as if it's holding a box on its knees.
The tarantula at the end of the opening credits is obviously nailed to the ground.
The night that Hogan uses the gunpowder to make enough light to see a mountain lion, it's clearly daytime, with a filter on the camera. The sky is blue above the trees.
The French did not celebrate Bastille Day, the 14 July, until 1880.
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.
There was no railway anywhere near Chihuahua in the 1860s.
In the tunnel scenes, Hogan and friends are using hand-held carbide lamps. Carbide was not produced in any quantity until 1892, and carbide lamps were not invented until several years later.
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.
When Sara encounters the rattlesnake and Hogan comes to her aid, there are some close-up shots of the snake and you can see the tail is being moved by a thin wire.
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.
When Sara is to remove the arrow from Hogan's chest. When she needs the knife and gun to slam the arrow through Hogan, there is a thin black wire attached to the tip of the arrow. Indicating it is being pulled to give the illusion it is being slammed through Hogan.
Shortly after Hogan saves Sara from the cowboys, he asks her which way she is headed. Her response is "North". She simultaneously gestures with her head and eyes directly towards the sun. Hogan then repeats the word and gesture. However, based on the length of the shadows, and the fact that Mexico is in the Northern Hemisphere, it is impossible that north is directly towards the sun. Hogan would know which direction north was, even if Sara did not.
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.)
Immediately after switching to the burro, Sara & Hogan arrive in a town along a dry creek bed. They dismount, and walk to their left up the bank, then cross a stone bridge over the creek to the market square. But they could have simply walked up the bank to the right, directly to the square.