When Munny and the kid arrive at the out house to kill the second cowboy under, the cloak of darkness, the shot in the scene from the rear shows the Kid animated and holding his nose while the ones showing from the front have them both still and no holding of the nose.
Several of the characters, including Little Bill and William Munny, are seen sometimes wearing shirts that button all the way up the front. This is incorrect for 1880/81, when men's shirts were still of the pullover variety, with or without a collar, and a small buttoned placket at the top.
Set in 1881. When the townspeople are forming a posse, they are discussing who will pay for expenses, and one of them says that the store won't sell them any more 30-30 shells unless they pay cash. The 30-30 was not introduced as a cartridge until late 1893.
Near the end of the movie, Jaimz Woolvett is talking to Clint Eastwood about how it feel that he just killed a man, Woolvett is drinking a bottle of Southern Comfort. Southern Comfort was not sold in sealed bottles until 1889, the film is set in 1881.
When we first see the train the whistle is heard blowing while the locomotive is in the shot, but there is no steam blowing from the whistle, which happens on steam engines whenever the whistle is blown.
When Munny is swearing at his horse in the rain (right after the "I would've killed you" scene in the jail house with Little Bill, English Bob and Beauchamp), Munny mutters "Sorry, horse," he can clearly be seen speaking emphatically after the line, but no sound is heard.
On several occasions, English Bob pronounces his erstwhile biographer's name as "Boh'champ". As an Englishman, he would have known that Beauchamp is one the few names that have idiosyncratic pronunciations (such as 'Chumley' for Cholmondley, and 'Urkurt' for Urquhart). He should have pronounced it 'Beecham' (with a silent 'P'), especially as he revelled in illustrating his English superiority over his American colleagues.
As Munny is getting beaten in the bar below, the Kid and Ned begin to flee the room. Ned falls out the window and rolls off of the wet roof and is heard landing in the mud on his back. When he jumps up, he's completely dry and not a bit of wetness, or mud/dirt on his back and arms.
English Bob says that no assassin would dare hold a gun to a monarch. There were, in fact, six assassination attempts made against Queen Victoria, and they were well known at the time. He certainly would have known about them, though it should be mentioned that he was concerned with successful attempts (looking at a monarch causes the hand "to shake"). However, it should be noted that English Bob was mainly saying this to antagonize people and not necessarily because he truly believed it.
After shooting the pheasants from the railroad car, English Bob holds the barrel of his Colt Peacemaker up and opens the side-gate of the cylinder, rotates the cylinder and the empty shells fall out. Empty casings cannot fall out of the cylinder as they expand during the discharge of the shell. The Peacemaker has a spring-loaded push-rod attached under the barrel to eject the casings from the cylinder after they are fired.
After Will and the Kid shoot the second cowboy and are riding away, the middle cowboy (kneeling) clearly fires shots in a different direction than the other cowboys, even though Will and the Kid are riding off in the same direction.
When Little Bill is reading from the Duke of Death book, you can clearly see that there is a script attached inside the book, with bright white paper and bigger print for him to be able to read the part.
When William Munny wakes up from his fever after being assaulted by sheriff Little Bill he sits outside the shack and talks to Delilah Fitzgerald. You can see the blue sky behind the house through springs in the wood revealing that it's not the same house/shack as in the first shot and the fact that it's a scene-set.
The goof items below may give away important plot points.
Near the end of the movie, Jaimz Woolvett is talking to Clint Eastwood about how it feel that he just killed a man, if you look at his coat, the buttons are Snap Buttons, which didn't exist in 1880/1. They weren't invented till 1885. They were considered specialty buttons and weren't commonly available till mid 1890s.
In the bar room shootout scene, many pistol shots are fired. The foley sound is correct. When Munny fires the rifle to kill Little Bill, the foley sound adds the classic "rifle shot" sound, with obvious echoes. In the enclosed barroom, there would be no echoes of the shot, just a loud bang.