Accidental Innuendo: Nick's line about Jimmy's extreme nausea: "I remember my first time. Shake it off, Neutron! Hah hah hah!"
Award Snub: Inverted. It was amongst the first nominees for the newly-created "Best Animated Feature" Oscar, against Shrek (which won) and Monsters, Inc.. Hardcore animation fans were offended that something so ugly and juvenile would be given such an honor.
Throughout the film, Cindy regularly refers to Jimmy by his first name; this is hilarious in the fact that in the TV series, she rarely does so, preferring to address him as Neutron (or "nerdtron", among other mocking nicknames), and this is lampshaded in the episode "Stranded".
One time, Goobot throws one of his henchmen out of the airlock, which the Junkman threatens to do to Jimmy, Carl and Sheen in his introductory episode.
Inferred Holocaust: No infants and senior citizens were present at the film's climax, which means they were left all alone in the town.... Some might have had older siblings, but can we expect all the kids to account for all the helpless babies?
Iron Woobie: Jimmy. He's constantly being picked on for his small size by other people, but that never stopped him from continuing on with his life and enjoying his small group of friends.
Every scene where the kids sadly reflect on the loss of their parents.
When the aliens take Goddard away from Jimmy as the latter calls out for his dog's name.
In the cell, where everyone becomes bitter towards Jimmy after realizing that this is all his fault. While Sheen and Nick start fighting, Cindy goes to Jimmy, who starts crying.
The Problem with Licensed Games: Almost averted for the PC game. While the game suffers from typical movie-based game flaws such as dated graphics, short playtime and clanky controls, it's actually creative in the way it adapts the original script and the humor is very Jimmy Neutron-like.