- The first scene of Noah's science class starts at 02:03 by zooming out from the balding spot on Rainn Wilson's head. Director Robert Shaye "wanted to indicate he was an aging hippie."
- The theme song to the movie, "Hello (I Love You)" (not to be confused with the similarly-titled classic song by The Doors) is a rare one-off song by former Pink Floyd frontman Roger Waters, whose songs are usually part of concept albums. Waters worked with composer Howard Shore, so that the song's melody is a leitmotif in the film, as well as dovetailing well with the rest of the film's score. Waters commented, "I think together we've come up with a song that captures the themes of the movie - the clash between humanity's best and worst instincts, and how a child's innocence can win the day." Incidentally, the film touches on themes that Waters' album Amused to Death was concerned with, while the song's lyrics reference Waters' Pink Floyd works Dark Side of the Moon and The Wall, as well as Waters' solo album Radio KAOS.
- The giant cockroaches that cover the surveillance camera lens at 71:47 on the DVD are not Computer Generated. Director Robert Shaye mentions in the commentary that the production employed three "cockroach wranglers" to handle the insects.
- Movie Goof (factual errors): Early in the movie, the science teacher Larry White (Rainn Wilson) tells his class that James D. Watson and Francis Crick "cracked" the genetic code. This is untrue. While Watson and Crick's discovery of the double-helical structure of DNA helped explain how genes were replicated during cellular or viral reproduction, Marshall Nirenberg, Har Gobind Khorana, and Robert Holley actually did the research that correctly interpreted the genetic code, for which these three scientists received the 1968 Nobel Prize in Physiology and/or Medicine.
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