The events upon which the story is based happened in June 1975. There is a portrait of Richard Nixon in the FBI director's office. Nixon resigned in August 1974. Gerald Ford's picture should have been there. Also, as Val Kilmer is driving in the opening sequence, "Badlands" by Bruce Springsteen is playing on the car radio. The album containing this song was released in June 1978. The car driven by Kilmer in the opening scene is a Ford Mustang convertible which wasn't released until 1983.
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 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.
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.
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".
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..
As Coutelle and his goons chase Levoi and Crow Horse towards the stronghold, they are supposed to be driving across virgin prairie, but we can clearly see the tracks in the grass made ahead of their Chevrolet Impala (early 80's model, and the film is set 10 years before) by the camera truck.
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.