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.
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.
Continuity mistake: In the classroom after Cindy is done explaining her dinosaur report she heads back to her desk, Jimmy and Cindy get in an argument when it cuts to Jimmy, in the background you see Carl standing up and not sitting. (00:09:40)
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.
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.
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.
Plot hole: When Jimmy is in his little rocketship launching his toaster satellite into space, the morning newspaper that his dad is reading already has the photo of the rocketship on the front page as a UFO. But the military jets were the first ones to spot the rocketship, the newspaper couldn't have gotten the story and printed it out that quick.