Movie Goof (factual errors): Archbishop Romero is killed at point-blank range by a handgun. However, the real Romero was shot by a sniper (though in the same circumstances).
Movie Goof (continuity error): The position of the gun in the red-shirted man's hand changes from lowered to 90 degrees with his body.
Movie Goof (factual errors): When the colonel approaches Boyle, he is sprayed with mace. Less than half a minute later, he has completely recovered.
Movie Goof (errors made by characters, possibly deliberate errors by the filmmakers): In the middle of the film, during Christmas, Cathy Moore says to Richard Boyle "you're 42 years-old." At the end of the film the border officer reports his birth date as being "2-26-43". As the story takes place during 1980-1981, Boyle would be 37 or 38 years-old during that time period.
Movie Goof (crew or equipment visible): At minute 41:44, when Major Max is giving his speech at the dinner table, as he circles the table you can clearly see the camera and boom operator reflected in the black window behind him.
Movie Goof (anachronisms): In the beginning of the movie, the main character (Woods) complains to his friend (Belushi) that San Francisco has become a "yuppie" town. The word "yuppie" is used frequently. However, the movie is set in 1980-81, and the term "yuppie" didn't become popular until 1983-84. An early, obscure use of the word from 1980 exists, but a syndicated 1983 magazine article is commonly viewed as the introduction of the term.
Movie Goof (revealing mistake): When Richard Boyle is being attacked by the thugs, you can clearly see that the blows do not hit him, yet he reacts as if it were so.
Movie Goof (revealing mistake): When the young man is executed while Belushi and Woods are in the armored personnel carrier, the gun is obviously pointed over the man's head.