These are all interesting examples, and I've tended to gloss over these points, too, preferring to focus on the characters, like most people. But...
One that has always made me scratch my head is the timeline of getting camp broken down and moving the sheep down the mountain after Aguirre's second visit. In the screenplay, much of the action seems meant to take place on different days, but as it plays in the movie, it seems to be on the same day.
We see Ennis wake up in the pup tent in the morning. At what seems to be mid-morning of the same day, he arrives at camp, and instead of getting breakfast, he sees Jack taking down the tent. (In the short story, this takes place the week after the big snow.) Then, at what seems to be mid-afternoon of the same day, we have the lassoing/tussle scene, followed by a shot of them taking the sheep down the mountain.
Logically, Aguirre would not have gotten to Jack that early in the day to give him the news, and even if he did, Jack would logically wait for Ennis to show up and have breakfast before packing up. (Even if he struck the tent before breakfast, by the time they got completely packed and rode up to the sheep, it would be very late in the day to start taking them down.) If, instead, Ennis is arriving for supper, Jack wouldn't be taking down the tent, since it would be too late in the day to get all packed up and go back to the sheep to get them going. They would need to wait til morning. Now, there's no reason to assume the filmmakers ever intended this to be the same day, but that's what it looks like.
In fact, the screenplay puts the two scenes (Jack telling Ennis the news and the lassoing/tussle scene) on separate days, which makes more sense. The first scene is "Day" and the second is "Morning." By combining Jack's taking down the tent with giving Ennis the news, it seems to me Ang cheated us out of a final Tent Scene.