After Maggie Eagle-Bear's son is shot in the arm, the volume and pattern of blood covers nearly his entire upper arm. In the next camera shot, the volume of blood is significantly less and a different pattern. In the third camera shot, the blood volume returns to the same as the first shot.
Bloodstain disappears from the right side of LeVoi's shirt.
When LeVoi places the injured child in Maggie Eagle Bear's arms, there are blood stains on his shirt at the left shoulder and on the right near his waistline. When he attacks the shooters in clinic parking lot, there is no blood on the right side of his shirt.
As Levoi walks into Grandpa Sam Reaches' trailer, the TV he is watching has very poor reception (static, etc.) In the next shot, the picture is clear and perfect.
The Wounded Knee memorial stone shown in the movie is a replica of the original, on which the 19th name was changed from "Swift Bird" to "Thunderheart". However, the 11th name was misspelled, on the original monument is "Yellow Robe" while on the replica is "Yellow Rose".
In the stronghold scene, one of the tribal traditionals (ARM members) is holding a rifle with a small white tag and string attached to the trigger guard. This small missed detail is presumably from the props department for equipment accountability.
As Coutelle and his goons chase Levoi and Crow Horse towards the stronghold, they are supposed to be driving across virgin prairie, but you can clearly see the tracks in the grass made ahead of their Chevrolet Impala by the camera truck.
After Ray and Walter walk away from the pow-wow campfire at Grandpa's, they start their little argument. After Walter says "they did", Ray says "Bullshit!" After that, you hear Walter say "You're bullshit!" but if you look closely, his lips don't move.
When Maggie Eagle Bear drives off, another camera crew is reflected in the cars window pane.
The boom mic is reflected in the windows of the car Agent LeVoi ducks behind when he chases Jimmy Looks Twice into the trailer before his escape.
FBI agent Ray Levoi is leaving D.C. for South Dakota but when they show his plane take off, LAX's distinctive control tower is clearly visible.
The original version shows Val Kilmers character drinking peyote; now that scene has been cut and it makes no sense. Why is he freaking out and having visions in the fire. It destroys the whole point of the movie in that the Val Kilmer character couldn't use logic, etc. to solve the case and had to try something else and learn his 'spiritual' background and get help from the 'spirit world' beyond our normal perceptions... Now it's just some guy acting weird because of a fire... It doesn't explain why he pulls his gun and the Indian sheriff tells him 'I know you're scared'... it was because he was having peyote visions; which are now censored, because all you belong in the soul harvester machine and if you dared take peyote you might learn that truth..
Although LaVoi tells his partner in the first ten minutes that he doesn't smoke, a pack of cigarettes are clearly visible in his t-shirt pocket in the final scene when he confers with Crowhorse.