After Calvera and his men are driven from the village the first time, there is a sequence in which three of his men start taking potshots at the villagers from the trees. One of these shots strikes Chico's hat and knocks it off his head. He even sticks a finger through the hole after retrieving it, however in a scene just a couple minutes later, Petra (the Mexican girl) is talking with Chico. We can see there is no bullet hole in the front of his hat and at one point, he turns his head 180 degrees in order to look behind him and there is clearly no bullet hole in the back of his hat, either. It has simply disappeared.
The knife used by Britt appears to be a stiletto switchblade (automatic opening knife with locking mechanism). This kind of weapon was brought from Italy only in the '50s which is about 100 years later than the action of this movie.
The flute which Barnardo carves and gives to the little girl has no fipple, the hole down from the mouth end which produces sound when air is blown across it. Despite this he is able to produce a reasonable tone and distinct notes: clearly dubbed.
The first man Calvera kills near the beginning of the movie has no wounds on his back after being shot and falling to the ground. When the villagers run to the body to look at the man, there are two wounds on his back.
As Chris and Vin ride the hearse back from the cemetery you can see one of the tassels fall from the head of the horse on the left. In the next shot the horses are coming around a corner and the tassel is back in place.
After Britt throws the knife into the cowboy in the rail yard, two train engineers are seen leaning out of the engine's window observing the scene. In the next shot, one of the engineers has moved to the platform between the engine and the tender car.
During the final battle we see Bernardo slumping off a roof, onto a clay-tiled awning, and then crouching behind a brick wall. We next see him when he shoots a guy who is about to mount a horse. The guy ends up with blood only on the back of his shirt. If Bernardo shot him in the back we should see either Bernardo, the clay-tiled awning or the short brick wall in the background. If Bernardo shot him from any other angle there should be blood on the front or sides of the guy, not just on the back.
When Chris and Vin begin driving the hearse up to Boot Hill, they pass the Belmar Hotel sign twice - once silently at the very start, and then again as they briefly discuss the towns they've come from a few moments later.
After the first defense of the village, when Chris is asked what he would do if he were Caldera, the villager behind him with the sling has the sling going over his left shoulder. After the Chris tells the villager to change the guards, the villager with the sling has the sling over his right shoulder.
The first man that Calvera shoots puts his hand to his chest after the first bullet. As the second bullet fails to make an inbound wound in his chest, it must have hit his hand, yet he clear has no wound to his left hand shown then nor afterward.
Just before Vin walks away from the craps table in the bar, the cowboy at the end of the table rolls the dice. In the very next shot the same cowboy is shown throwing the dice again without having retrieved them.
When Chris and Vin are returning from the cemetery on the hearse, they come to a stop and get off the hearse. As the camera pans slightly when they're getting off the hearse you can see a piece of wood used as a chock (looks like a 4"x4") placed in front of the right rear wheel of the hearse. There was no one around to place the chock under the wheel.
The goof items below may give away important plot points.
In the last scene, when the three village boys put flowers on Bernardo's grave, the middle boy makes the sign of the cross from right to left, as they do in the Eastern Orthodox church. The other boys do it correctly, from left to right.
When Lee regains his nerve and prepares to enter the building where the villagers are being held captive he holsters his single action Colt revolver. In the next scene he is seen breaking through the door, sweeping aside the bandits gun he draws his own gun, which is clearly a Smith and Wesson double action. He disposes of the bandits using double action, just pressing the trigger without first cocking the hammer which is required with the single action Colt. He walks out the door with the single action gun back in his hand, is fatally shot, flips the gun out of his hand and dies face first against the wall.
When Calvera gives the "adios" command to send the seven out of town, he waves his right hand and starts walking away from a pole. In the very next shot (from behind) he is shown still leaning against the pole.
After Chris delivers the final line, Vin and Chris turn around and ride over the hill - Chris is riding on the right. After a brief cut away, the camera cuts back to them riding into the distance and Chris is now on the left.
Harry Luck (Brad Dexter) gallops back into town to help the seven during the final battle, jumps off his horse, runs to the doorway of the building they're holed up in and is then shot by Calvera's men. "Harry" is very obviously a stuntman, as Dexter is taller and quite a bit heavier than the man in the scene.