When being harassed by the press, Kitty tells them that her father owns all the pineapples in Hawaii. A moment later, Billy Flynn says that her mother owns all the pineapples in Hawaii.
After "Funny Honey", the on-stage lights go down, meaning you can see through the scrim. This reveals the silhouette of Fred Casely's actor getting up to read an ensemble line for the following scene. Because Fred Casely was just murdered, the audience reacts audibly to this, and someone in the audience even says "He's alive" in an amused tone.
There are a few instances where you can see the outlines of cast and/or crew members behind the scrim despite the lights on stage being on, which is meant to hide everything behind the scrim.
Actors can be seen breaking character a few times, such as when two ensemble guys come out with signs during "Razzle Dazzle" and when an actor's voice cracks during the Courtroom scene.
Techs can be seen moving set pieces after they were supposed to be moved leading during Roxie and Velma's "Nowadays" duet. The lights behind the scrim were on, so this, along with Roxie and Velma standing off to the side, is clearly visible. This hiccup appears to have only occurred on this performance night, as it does not occur in the unofficial closing night recording.
Amos and Billy talk over each other a few times during the scene in the middle of "Mister Cellophane"
In the scene placed during "When You're Good to Mama", Velma is seen holding a modern newspaper article about the legalization of Cannabis. "Chicago" takes place in the 1920s and, while marijuana was popular at this time, the topic of legalization was not commonplace. This newspaper is also in color.
At the beginning of act two, Velma says that Roxie is being looked over by the state medical examiner to investigate an alleged pregnancy. This pregnancy is not real. It's shown in the 2002 film adaptation of Chicago that Roxie convinced the examiner to tell that the baby was real to the jury by having sex with him, but no explanation for why the examiner didn't blow the whole thing open is given here.