Continuity mistake: Nick's necklace is a string looped through a ring, but sometimes the string makes only one pass through the ring and sometimes two.
Continuity mistake: When Jimmy Neutron is giving birthday presents to his mum he pulls out a necklace and some earrings from a bag. His mum only takes the necklace from him but the earrings are no longer in his hand. (00:20:10)
Continuity mistake: In the opening sequence, Jimmy uses a long string from Carl's shirt to help launch the satellite. Jimmy then launches Carl from the rocket. That same morning, Jimmy finds Carl hanging from a tree, and his shirt is intact.
Character mistake: When Jimmy explains to the kids of the town where the aliens took their parents, he mentions the origin of the aliens being somewhere in the Orion Star System, 3 million light years away. The Orion system is way closer than that. It is actually less than 1400 light years away from Earth. 3 million light years away would place them further than the Andromeda Galaxy.
Factual error: When Cindy is giving her "fossil-to-chromosome ratio" report, she calls her model dinosaur skeleton a plesiosaur. However, the skeleton is of a bipedal dinosaur (likely a hadrosaur, judging by the "duckbill"), while plesiosaurs were aquatic reptiles with flippers instead of feet.
Continuity mistake: When Jimmy goes to check his experiments, there is a fish tank type thing and he then checks the invisible hamsters and the girl eating plant, but when he gets to the burping soda the fish tank thing is gone.
Plot hole: When the aliens kidnap the adults, the kids are left behind. But all the kids seen are around 11 and younger. Where are the teenagers or young adults? None of them are during the celebration scene nor in the arena on the alien planet.
Plot hole: At the beginning of the movie, Jimmy's rocket could barely stay in one piece, much less leave the atmosphere. And that was only one rocket. But later on, not only can he build a much better rocket from one of the rides in the amusement park, but he can build ones for the other kids as well. It's not like he got better at building rockets, he tried to build another one in his yard before he and the town's kids did, but it fell apart.
Other mistake: The size of the town Jimmy lives in is inconsistent with the size of the population shown. The town is quite big if it has its own mall, amusement park, and a large elementary school. Yet combined with the kids and adults seen, there couldn't be more than a hundred people living in this town.