In the studio, right before a 1969 concert, the Doors' manager tells Jim Morrison "I am not going to go through this again with you, and lose you at the bottom of a bottle of Southern Comfort like Janis [Joplin]." The next scene takes place in spring 1970. Janis Joplin died October 4th, 1970.
At the Miami concert, Jim Morrison has a boom stand for his microphone. After a cut to an audience shot, the camera goes back to Morrison, with no microphone stand. After another audience shot, the camera returns to Morisson, and the microphone stand is back.
When Jim Morrison is chasing Pam around the room, he throws a lamp and knocks a picture partially off. It swings back and forth. A few seconds later, when Pam throws a glass at him from behind a chair, the picture is back up, and only slightly tilted.
After Jim Morrison has chased Pam around the room, he grabs her and asks if she will die for him. A curtain is blowing behind him. A few seconds later, the curtain is no longer blowing. When Jim opens a window, there is no wind.
In the film, the New Haven concert is a sold-out show, in a beautiful theater with a balcony. In real life, the show was at the New Haven Arena, a broken-down hockey rink with no balcony. It was also half-empty.
In the film, a female photographer sexily encourages Jim Morrison to take his shirt off, resulting in the iconic "Young Lion" photo first seen in the Village Voice, and later used as the cover photo for the Doors 1985 "Best Of" album. The photographer was actually a man, Joel Brodsky.
As with most biopics, some of the events did not occur exactly as they are portrayed in the film, or may have happened at a different time. Some did not take place at all and are included purely for dramatic purposes.
Jim Morrison says "Well we're a sullen group, Ed" without moving his lips. It was done deliberately, to allow the audience into Morrison's thoughts for a moment. If he'd said it directly to Ed Sullivan, he would have been thrown out immediately. Instead, the audience is allowed to hear him think it, which lead to the mischief Morrison got up to on live TV.
During the magazine photo shoot, Jim Morrison begins to wander around the studio with the photographer following him, still taking pictures. A flash continues to go off, yet there is no flash on the camera, they are still on the stands on the set.