The show mentions many times that the robots' arms don't work. Sometimes they have completed projects that require working arms, or they perform deeds with their arms moving.
In many episodes, the host and bots audibly turn the pages as they go through their scripts.
For several seasons, two torches appear in the hallway as the camera enters and exits the theater. The flickering changes direction, proving that the entries and exits are the same shot run forward and backward.
During the theater sequences, Crow frequently talks without moving his mouth. Sometimes his mouth moves after he finishes talking.
Joel and Mike's head mics are often visible when they turn their heads during theater sequences.
The rod used to control Tom Servo is often visible when he is carried into or out of the theater.
A line in the end credits thanks "The authors of the First Ammendment." The last word should be spelled "Amendment."
The line, "I thought you were Dale!" is used as a riff in many episodes when a scene involving hands is shown in the movie the characters are forced to watch. The line is supposed to reference an Ivory Liquid commercial involving an older woman's "young-looking" hands. However, the line was actually said in a Grape Nuts commercial involving an older woman's "young-looking" body.