After Jones follows the hawk back to his family he sits on the ground talking to Maggie. The wind blows Jones' hair and doesn't mess up Maggie's hair even though they are a few feet from each other. When the wind blows, Jones' extension clips can be seen and his "real" hair blows above his head, as it is much shorter than the extensions.
When Kayitah is killed by multiple blows with the wooden club there is much blood and it is implied that he has been hit in the head. When "Kayitah's ghost" rides his horse, his face has just a little blood near the mouth. His head and face are clearly recognizable, rather than being completely disfigured from the blows to his head.
Ray McKinnon's character, Russell J. Wittick is seen during the final rescue, although he is supposedly dead at the time.
When El Brujo puts the dirt in Lilly's mouth, the rope used to gag her is across her nose but in the next shot it disappears.
The scar over Maggie's left eyebrow changes position and color throughout the movie.
When Jones is following the hawk, its shadow is extremely large, which is meant to imply the altitude of the hawk. Since the difference in distance from the sun from Jones and the hawk is virtually non-existent, the hawk's shadow should be its actual size.
The "Brujo" scaling the cliff side is attached to a rappelling rope (visible in the three alternate endings).
Several riding shots of Dot are clearly done by an adult woman in a wig.
After finding the photographer's wagon, an owl is seen sitting in a tree. As the owl flies away the sound of wings flapping is heard, When an owl flies, the wings are totally silent.
Right before Maggie get's ready to operate on the Indian, Dot finds a tortoise and picks it up. The tortoise is a Sulkata, or African Spur Thigh, not a Desert Tortoise, which it should be, and would never, ever be found in the New Mexico desert.
Incorrectly regarded as a goof: The size of the hawk's shadow appears much larger than would be seen normally. The shadow of the hawk is a product of Jones' imagination and would be of whatever size his imagination would see it. The effect of the drug and the character's imagination produce the hawk leading Jones to his family.
When Samuel speaks to the bird sitting next to him, the bird has a yellow plastic ring around its right ankle.
Even though the film is set in the 1800s, in one of the panned shots near the homestead, there are distinct, tightly-spaced logging roads visible on one of the distant hillsides.
The pack horse wears a brass-buckled English leather halter (modern type of halter) throughout the movie.
When the Indian kidnappers are riding through the desert, just before they return to the cave where they are hiding out, a dirt road is clearly visible running from upper right to lower left across the entire screen.
Jones and Dot were wearing hats before they were washed downstream during the flash flood. But when they were climbing out of the water onto dry land, they weren't wearing their hats. In the next scene when they were riding their horses they were wearing their hats again. There is no way they could have found their hats after the flash flood.
When the telegraph operator is sending and receiving messages, there are only a few clicks per word. However Morse code is several (2-6) clicks per letter.