Bob Dylan decided he did not want to be in the film 15 minutes before he was due on stage. His reasoning was that he did not want to have two films he was in (the other was Renaldo and Clara (1978)) competing with each other at the box office. Bill Graham, owner of the Winterland, intervened and Bob decided to play. The conditions were that only the last two songs of his performance could be filmed.
The Band's management had overbooked the show. Two days before the show, they tried to have Muddy Waters taken off the bill. Levon Helm, The Band's drummer, threatened not to play the show if Muddy Waters was asked to leave. Muddy Waters is in the final cut of the film.
Guitarist Robbie Robertson's microphone is off through most of the show. He is seen singing at full strength, but no vocal from his microphone ends up in the film. (When Neil Young is singing the first verse of "Helpless," Robertson can be seen in the background mistakenly launching into the chorus as Young continues the verse. The words sung by Robertson are unheard despite the nearby microphone, and bassist Rick Danko can be seen telling Robertson he came in too soon.)
During the performance of the song "Mystery Train", performed with Paul Butterfield, the stage lights blew out, leaving only one spotlight to light the stage. When Neil Young performs "Helpless", Joni Mitchell is singing background vocals from a microphone backstage.
In the interview where Helm and Robertson talk about their first time in New York, Robertson states that they stayed in the Times Square Hotel located on 42 Street. The Times Square Hotel is actually located on W. 43 St between 7th and 8th Avenues. The building has since been renovated into apartments but the lobby and most of the building remains true to its hotel roots and is still named the Times Square.