Lou Diamond Phillips was dragged by a spooked horse when filming a new scene. He broke his arm and a kneecap. The horse was spooked when Emilio Estevez fired a gun and threw Lou off. The horse then ran, dragging Lou by the noose around Lou's neck and tied to the saddle horn. The scene was never re filmed. Lou talks about this incident on Celebrity Close Calls (2010).
Emilio Estevez plays the role of Brushy Bill Roberts, an old man claiming to be Billy the Kid. Initially Estevez had a lot of trouble convincing the crew and studio that he was capable of doing it. While the studio looked into hiring someone to play the role, Estevez hired a make up artist and a dialect coach to help him out. Estevez's transformation into a very old man convinced them to use him after all. Estevez even tested his disguise by going to play dominoes with some people off set, and they did not disbelieve him when he lied about his age.
Emilio Estevez originally approached Jon Bon Jovi to ask him for permission to include the song "Wanted Dead Or Alive" on the soundtrack. Bon Jovi didn't feel the songs lyrics were appropriate; however, he was inspired by the project and resolved to write a new song for the film that would be more in keeping with the period and setting. He quickly wrote the song "Blaze of Glory", and performed it on acoustic guitar in the New Mexico desert for Estevez and John Fusco.
Although the movie depicts Pat Garrett and Billy the Kid as close friends who were at one time partners in crime this is a considerable stretching of the truth. In reality their association was much more casual in nature stemming from their mutual patronage of Beaver Smith's saloon in Fort Sumner where they were both avid players of the card game Casino. They had a cordial acquaintance with one another but were never close friends nor did they ever ride together as outlaws.
No one got away from the ambush by Garrett's posse at Stinking Springs. A few were injured, and Charlie Bowdre died. The Kid and his gang surrendered and were all taken to jail in Santa Fe, but Dave Rudabaugh eventually escaped and did flee to Old Mexico. Despite claims that he fled to Montana and led a "normal life", it is accepted that Rudabaugh killed two men in Mexico and was shortly thereafter beheaded. The Mexican government even took a picture of his severed head as proof that they had executed the outlaw.
When Billy says "Quien es" ("Who is it" in Spanish) during the introduction of Tom O'Falliard, it's a possible homage to the real Billy the Kid, who reportedly said those same words before he was shot by Pat Garrett.
In one scene, Arkansas Dave derisively calls Chavez a Mexican. Chavez responds with "Mexican-*Indian*, you son of a bitch!". In the first film, Dirty Steve derisively calls Chavez a Mexican, to which Chavez responds, "Mexican-Indian, you son of a bitch!".
A self-proclaimed joker on set, Estevez had suffered from a lot of practical jokes at his expense by Kiefer Sutherland and Lou Diamond Phillips on the set of Young Guns (1988). During the shooting of Young Guns II (1990), Estevez took his revenge on Sutherland when Sutherland was filming a scene in a bath tub. When nobody was looking, Estevez slipped a Baby Ruth candy bar into the tub, so that it slowly rose to the surface during Sutherland's scene. Estevez later remarked in an interview that if a joke is done against him, he will make sure another is done in return regardless of the time in between.
Jon Bon Jovi wrote the song Blaze of Glory specifically for the movie and was so inspired that he went on to write an entire album, of the same name, which charted at Number 3 in the US. The song was immediately chosen as the movie's theme song and was a Number 1 hit on the Billboard Hot 100. Jon also had a cameo in the movie as the dirty, long-haired prisoner that is shot in the chest & blown backwards as he's climbing out of the pit in the lynch mob/rescue scene.
With the exception of Dave Rudabaugh, many of the gang members who did follow Billy the Kid both during and after the Lincoln County War did not appear in the film including Billy Wilson, Tom Pickett and Charlie Bowdre, the latter having been killed off in the original film.
In the movie Pat Garrett & Billy the Kid (1973), James Coburn (as Pat Garrett) says the line: "Why don't you take your money, shove it up your ass, and set fire to it." In 'Young Guns II', James Coburn (now in the role of John Chisum) says: "Well you can take those figures, and shove them up your arrogant little ass, and set fire to them."
William Petersen (Pat Garrett) has played two of the Kennedy brothers in his career. Emilio Estevez (Billy the Kid) would later go on to make Bobby (2006), a movie about Robert F. Kennedy. The film would also reunite him with Christian Slater (Dave Rudabaugh).
The last thing heard before the screen fades to black at the end is Billy the Kid's (Emilio Estevez) unique laugh. In Amadeus (1984), the last thing heard before the screen fades to black is Mozart's (Tom Hulce) unique laugh.
Doc Scurlock (played by Kiefer Sutherland) is shot in the chest as he is leaving the hideout. In reality, it was Charlie Bowdre who was killed in that fashion. The character of Charlie was killed off prematurely in Young Guns (1988).
Some reports show when the real Billy the Kid was arrested and put on trial, he did not tell the judge to go to 'hell hell hell' as is depicted in the film. He kept his head down and when he was asked if had anything to say, he answered simply, "No". Other reports show it happened exactly as depicted.