At the Forest Service station, Jerry G. pulls out his service revolver to prevent Joe from taking his cow. The gun is pointed directly at the camera and one can see that the chambers are empty. When Sheriff Montoya intervenes, the revolver is fully loaded.
As Bernie pulls up to the Forest Service office during the scene with Joe's cow, his truck creates a large dust cloud which sweeps over everyone. In the next shot, the cloud is completely gone.
When Armarante is in the bar in the morning, he is served a shot of whiskey. He drinks it and says, "I'm not saying it's good. I'm not saying it's bad." In the next shot, his shot glass is full again and he drinks the whiskey again. It was not refilled by the bartender.
As Amarante Cordova walks into the bar, the bartender places an empty shot glass on the bar for him. The next shot shows Amarante from behind walking toward the bar, and the bartender places the empty glass on the bar again.
When Ladd Devine and his wife lie on their bed and he talks about the situation getting out of hand, Flossie is lying with her back to the pillows for two shots, then suddenly turned towards him in the next shot (and the remaining two of the scene).
When the Miracle Valley welcome sign is shown burnt down, there is a strong disruption to the picture, probably from the camera being hit.
At the end of The Milagro Beanfield War (1988) when Joe is handcuffed, Montana says "i hope there is no trouble for your sake," then you hear Bernie Montoya say "Montana, the key." This phrase is repeated a little later as Montana is walking away after being called back by the governor and Montana tosses the keys high in the air.
Camera shadow is visible during the final dance.
Twice in the film, a character mentions El Paso as an example of a big city. Milagro is supposedly in northern New Mexico and the locals would naturally refer to Santa Fe or Albuquerque, not a city 400 miles away in Texas.