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.
Broken Base: The debate on whether the movie should have won nomination for Best Animated Feature or not divides people till this day. Some say it's a cute story with memorable characters that definitely deserved having more people hear about it, others contend it was absurd to give an animated feature with obviously dated animation (and not just compared to the very same year co-nominees) so much praise in a contest for, well, best animation. Then there are those who love the TV series and think it's much better than the movie.
Inferred Holocaust: No infants 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.
The Problem with Licensed Games: Almost averted. 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.