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.
Bowling for Soup's rendition of the shows theme song.
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. And there are others who, while liking or even loving the movie just fine, think it didn't need a nomination. Though considering how much the Best Animated Features in recent year usually lean toward mostly Disney fare (and even that isn't always exempt i.e Wreck-It Ralph losing to Brave on the suspicion that the Academy wouldn't recognize a video game film despite it's story being consider better. A sentiment likewise shared when The LEGO Movie wasn't even nominated for supposedly being too commercial), this has cause the debate to go down in years since most animation fans favor creativity in conjunction with pretty visuals rather then just the latter by itself. It can also be forgiven considering it was an early category.
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.
Moral Event Horizon: Goobot crosses it when he reveals the parents of the kids are going to be sacrificed to Poultra, and how it's all Jimmy's fault because of Jimmy's transmission.
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. 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.