Miscellaneous: At the end of the dance number "All For The Best", Joanne moves her arm the wrong way and quickly corrects herself.
Revealing mistakes: In the final scene when the troupe is carrying the deceased Jesus around the corner, and the streets of Manhattan are still supposed to be vacant, a person can be seen walking on a sidewalk in the background.
Continuity: The face paint that Jesus puts on all the characters in the junkyard changes in almost every scene after that. The position and even some shapes change.
Revealing mistakes: When Jesus is painting the symbols on the apostles' faces, on some of them, the brush isn't making contact with the face and Jesus is painting entirely different symbols. Also, he uses different paint and the symbols appear as different colors.
Miscellaneous: The conceit that New York City is magically empty of people (other than Jesus and his disciples) is messed up only once - during the baptism scene on Bethesda Terrace, a man in the background of Central Park Lake can be seen frantically trying to row his boat out of the camera's view (he is visible in 3 separate shots).