During initial filming, Video Assist Operator Ben Hunt shared with voice actor Rob Paulsen that he had memorized the Animanaics song "Yakko's World" (sung by Paulsen) back when he was in High School. Rob asked Ben if he wanted to sing it together and they did. Between takes of course.
The script supervisor on set could not stop laughing at the line "Don't worry Bunhead!" Every time. Every take.
The animation format used to animate thumbs was later used to animate Steve Oedekerk's tongue in Kung Pow: Enter the Fist (2002).
The "Yoda" puppet cost approximately $5000.
The naked thumb pilot in the thumb fighter jet was improvised on the spot, on set, while filming various thumbs and costumes.