Early in the film, during the bad guys hooraw through tin-panner's camp, one member of the gang is clearly shown shooting a 1872 Colt Single Action Army revolver at a steer. The film is set prior to the availability of the SAA and all other revolvers shown throughout the film are Colt cartridge conversions of the 1860 Army model, or the Preacher's cartridge conversion Remington.
When Barret throws a stick of dynamite into the tent, it lands near the front of the tent. The explosion comes from inside the tent. After the explosion the lit fuse of the thrown dynamite can clearly be seen.
When Hull Barret rides into town by himself on the wagon he is fine. When riding out with The Preacher after the fight you can see a cast on his arm. It is also visible as he mounts the wagon. Back in camp, it's fine again.
When Hull drives off in his cart after visiting town and being saved from a beating by the Preacher, a modern white bandage and finger splint can be seen on Hull's left hand. It disappears in later shots.
One of Stockburn's bad guy deputies, actor John Dennis Johnston, appears earlier in the film as one of the pan-handlers, during Michael Moriarty's night-time fire-side speech about not taking the $1000 to get out of town.
At the end of the film, after Megan rides the buckboard back to town and she learns that the Preacher has left, she is advised that she'd kill the horse team to push them any further. A few minutes later, after she calls to the wilderness, she and another character get on board and drive the horse team after all.
When Stockburn and his six men gun down Spider, they fire more than 60 rounds. Since none produce a second revolver, the most they could have fired was 42, more likely 35, leaving one chamber empty for safety.
When the preacher approaches Stockburn he unlocks his firearm to re-chamber it. The bullet chamber he chooses is visibly empty yet he locks it in place and kills Marshall Stockburn. However, this could be a deliberate choice by the filmmakers, in line with other suggestions that the Preacher is some kind of mystical character.
In the final showdown, Stockburn is shot several times by the Preacher. In the next shot, small rivulets of blood are shown running out of the bullet holes. Considering that Stockburn is wearing a trenchcoat over a suit, it's unlikely blood would just trickle out onto the coat like that - not to mention a gunshot wound would probably bleed a little more profusely.
When the Preacher shoots Stockburn at the end of the movie the camera angle shows his back and you can see the bullet holes on the left side of his coat, when Stockburn is shown from the front the bullet holes are on the right side of his coat.
The goof item below may give away important plot points.
When the preacher shoots Stockburn, bullet holes can be seen at the back of his trench coat. A few moments later as Stockburn is collapsing, there are no holes in the rear of his coat. When Stockburn is finally on the ground, the holes in the rear of his coat are present again.