Leading up to the final gunfight, there are several close ups of Angel Eyes' hand creeping toward his gun. The gun is clearly a Remington percussion type, but there are cartridges visible on his gun belt.
In the store scene with Tuco, he and the owner pass by several crates of black powder marked "ACME." ACME was a generic name for companies that came into use in the 1920s to enable them to appear on the first page of most phone books. It would not have been in use in 1862.
In the prison camp scene where the musicians are playing while Tuco is being beaten by Angel Eyes, the fiddle has fine tuning adjusters on the tail-piece. These fine tune adjusters were designed for metal strings used many decades later.
The movie takes place in early 1862 but the Union forces use at least one Gatling gun which would not have been put into the field this early in the war.
In early 1862 the gun was barely finished and the weapon wasn't patented until 1865. The U.S Army did not adopt the weapon formally until 1866.
A majority of the characters load metal cartridges into converted Civil War model revolvers. While this conversion did become commonplace in the late 1860's, back in 1862 metal cartridges hadn't been fully developed for those kinds of revolvers yet and paper cartridges were still the norm.
In one scene, Tuco praises Lee and damns Grant out loud to the troops coming out of the desert. However, the movie takes place during Confederate invasion of New Mexico Territory in February- March of 1862, when both Lee and Grant were unknowns at this time. Lee didn't assume command of the Army of Northern Virginia until June 1862. Grant was a relative unknown when he won his first victory at Fort Donelson in February, 1862, hardly enough time for Tuco and Blondie to know who he was. That being said, in another scene, Angel Eyes mentions Confederate abuses in Andersonville Prison, which only became a prison and started accepting prisoners in February 1864.
When the POW camp commandant is upbraiding Angel Eyes for his treatment of the Confederate prisoners, Angel Eyes responds with a comment about the treatment of Union POWs at Andersonville. Andersonville was opened in 1864. The Film is set in 1862.
The POW band guitarist is shown strumming his instrument, but the soundtrack guitar is "finger-picking." There are other mis-matches in the scene, including actors playing valve trombones which aren't heard.
Tuco is ambushed by three bounty hunters with one of them firing an anachronistic Winchester rifle at Tuco to make him fall off his horse. The bounty hunter with the rifle is heard working the loading mechanism yet when he enters the frame he is seen pulling the hammer on the rifle. If he had really used the loading lever of the rifle the hammer would have already been pulled down.
When Blondie is comforting the dying Rebel soldier near the end of the film, he gives him two puffs of his cheroot cigar - it changes length by almost an inch from shot to shot, first longer, then shorter, then longer again
Blondie and Tuco walk down the street of the desert town to confront the Angel Eyes' gang. At the beginning, their shadows are projected to behind them. Next shot, the shadows are projected in front of them.
One of the three bounty hunters that shoots Tuco's horse has a piece of grass in his mouth just prior to been shot by Blondie, that was not there in the previous frames when he tells Tuco he has a face worth 2000 dollars.
When Blondie and Tuco are carrying the explosives on the stretcher, at first the stretcher is missing several wooden slats, but as they approach the bridge, it changes into a completely different stretcher with no missing slats.
When Tuco enters the gun shop, he hangs the "CLOSED" sign at a downward-right angle on a nail on the back of the front door. As he exits the shop, the "CLOSED" sign is angled slightly down to the left.
At the start, when Angel Eyes is first seen, the boy stops the burro and the well's cross beam is in front of, and slightly above his head. In the next shot of the boy, the burro hasn't moved but the cross beam is now behind his head.
When the rhythmic music stops and Tuco is choking after screaming "Blondie", a person walking to the left can be seen on the left side of Tuco's face. You can also see a sun reflection on something carried by the person.
When Tuco prepares a bath that's been deserted, he pours bath salts into a tub already full of water. When the bounty hunter enters, Tuco is in the bathtub covered in bubbles. Pouring bath salts into an already filled tub doesn't create bubbles, especially when the water is cold.
When the two armies battle at the bridge, the Confederates are using the flag with the blue criss-cross on the red field. This is not the Confederate national flag, rather it is the banner of Gen. Robert E. Lee's Army of Northern Virginia. It would have been in battles in the east, not in the west.
The man pointed at as the Confederate General Sibley (by the hotel owner) is actually a Confederate Captain according to the rank insignia on his collar. The buttons on his uniform is furthermore misplaced compared to that of a authentic Confederation Captain. A genuine uniforms buttons would have been closer to the chest.
The character "Jackson/Bill Carson" is referred to as a member of the 3rd Regiment in the Confederate Army. During the New Mexico campaign the Confederates deployed the 2nd, 4th, 5th, and 7th Regiments of the Texas Mounted Rifles and some unnumbered territorial groups. There was no Confederate 3rd regiment of any sort, although the 3rd U.S. Cavalry did participate on the Union side.
In the retreat scene in the town a large unit of Confederate foot infantry is shown as marching with the retreating column. In reality, Sibley's force consisted entirely of mounted units and a single battalion of artillery. No foot infantry were used in the campaign on the Confederate side.
Blondie's rifle is a Winchester, which was not available when the movie is meant to take place, but the production took the pains to remove the wood fore stock to disguise it as a Henry which were available.
During the bridge scene with the explosives, the fuse is often seen in the water. Would this mean it could not burn? No, because fuses were coated in wax, lots of mine & tunnel work back then occurred in damp & wet conditions.
When Tuco and Blondie ride their coach up to the mission to recuperate from the desert several power poles are visible in the background to the left. (May only be visible in the wide-screen version). However, one can make the assumption that these are telegraph lines since the telegraph was a common form of long-distance communication during the civil war. Power poles are even visible by the train tracks when Tuco escapes his captive which makes sense since telegraph lines were commonly built along railroads.
When the runaway Confederate carriage first appears in the desert you can see someone steering it. Then, as Tuco seizes the horse-team to stop the carriage, the reins are obviously being held by the out-of-frame driver. In the next shot, viewed from the driver's bench, the reins visibly tighten to halt the horses and then drop.
During the preparation of the charges on the bridge supports, they are connected in series, and Blondie lights only one (too short) fuse. When the bridge blows, all four charges detonate simultaneously, since they were detonated electrically.
In the final scene when Tuco is shot down by Blondie, the position of the rope changes while hanging around Tuco's neck. First it is hanging vertically in front when he steps into the courtyard. Then it is slung over his left shoulder in the close-up.
At the end of the movie Blondie flips up the long-range leaf sight on his rifle but the cross member is so loose it falls down to the very bottom. This would give him no elevation of the gun barrel to allow for bullet drop, at the 1000 yards he must have been at, to make that shot.
If each gold coin had approximately 1 troy ounce of gold in it worth $20, $200,000 implies there were approximately 10,000 coins in the eight bags that Blondie and Tuco recovered. The weight of those 10,000 coins would be (10,000 coins * 1 oz/coin * 31.1 g/oz * 1 kg/1,000 g * 2.2 lbs/kg) = 684.2 lbs. Each bag would then weigh approximately 85.5 lbs. Blondie is seen loading up his horse with the gold two bags at a time (170 lbs). It doesn't seem likely that a person could lift that much gold without much more difficulty.
During the final show-down by Tuco, Blondie and Angel Eyes at the cemetery, Tuco has no bullets in his gun but you can see a flash from his pistol when Blondie shoots Angel Eyes. However, this is the sun glittering on the barrel of his gun, not a muzzle flash.
When Tuco (Ugly) runs up to the carriage filled with dead bodies, he opens the gate to the carriage and looks in. It can clearly be seen that the guy lying to the left is clearly blinking, even though everybody in the carriage except Bill Carson is supposed to be dead.