The position of the gun in the red-shirted man's hand changes from lowered to 90 degrees with his body.
Whild Boyle is at the Embsay he lights Col. Hydes cigar twice during his conversation.
Archbishop Romero is killed at point-blank range by a handgun. However, the real Romero was shot by a sniper. Also, while he was shot while saying Mass, it was in a small hospital chapel, not in a large church as depicted in the film.
When the colonel approaches Boyle, he is sprayed with mace. Less than half a minute later, he has completely recovered.
At one point Boyle and Cassady are together taking photos, and Boyle asks to borrow a 24 or a 28 (i.e. a 24mm or 28mm camera lens). Cassidy lends him one, Boyle attaches it... but the problem is Cassady uses Canon cameras and Boyle has a Nikon. The lens wouldn't fit.
The plot has the assassination of Bishop Oscar Romero happening after the election of Ronald Reagan. But the former took place in March 1980 and the latter in November 1980.
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.
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.
When John Cassady and Woods are taking photos in the body dump John's Camera has a winder on it. He takes a photo then winds the film manually.
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.
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.
El Salvador doesn't have nearly as many cows as the film portrays.
The drive from San Francisco to Alameda to pick up Doc's dog is completely nonsensical. They are shown driving on North US-101 after the split that would take them over the Bay Bridge directly to Alameda. Then they drive south on the Embarcadero Freeway, meaning they had to drive through city streets just to get back from where they turned off. The final shot of the drive has them going back into San Francisco away from Alameda.
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.
At 28:10 one of the "dead" bodies in the landfill moves his head.
During one scene at the US embassy, an extra dressed as a naval officer briefly speaks with one of the characters. The extra, looking to be in his mid-60s or older, is wearing the uniform of a Navy lieutenant, a fairly junior rank that would typically be held by officers in their middle to late 20s. A lieutenant would have been removed from service in the case of such a lack of advancement in rank. Even in the case of limited duty officers, who typically come from the enlisted ranks in the Navy, a lack of advancement into their 60s wouldn't have been acceptable.
Boyle refers to rebels possessing Belgian FLNs. He probably means FALs.