Factual error: When the boys are sent back to the Cretaceous era, they come across a leptictidium, a small, bipedal mammal they call "Leppy." Leptictidium were not around in the cretaceous, they didn't appear until around ten million years after the dinosaurs went extinct, in the early Paleogene. They also lived in Europe, not North America.
The League of Villains - S3-E16
Factual error: As the villains are approaching to Earth, South America is shown just under Asia, connected to the Arabian Peninsula and the southern tip of India. The two continents are nowhere near enough to each other to be seen at the same time from space, much less connected. They are on opposite sides of the Pacific ocean, over 10,000 miles (16,000 km) apart. (00:06:45)
Continuity mistake: In the audience, Carl's parents are shown sitting in the second row behind Jimmy's and Cindy's parents. In some POV shots of the stage, however, they're still in the second row but are sitting behind Corky Shimatzu, who is sitting on the opposite side of the theater from Jimmy's and Cindy's parents.
Factual error: Jimmy tells Carl and Sheen they were sent back 200 million years and throughout the episode, they say they are in the Cretaceous period. The Cretaceous period actually started around 145 million years ago. They would actually be in the mid Jurassic period. Also, the tyrannosaurs didn't appear until much later in the Cretaceous, around 70 million years ago.
Normal Boy/Birth of a Salesman - S1-E3
Plot hole: Throughout the show, many characters state that Jimmy was responsible for the meteor almost destroying Retroville in the episode "Normal Boy", however, how would anyone even know that? The meteor was put on course after being hit by some kitchen objects shot into space by Jimmy's orange juice machine. Neither Jimmy nor his parents or anyone saw the objects go into space, much less witness them causing the meteor head straight to earth, especially since the meteor wasn't detected until the next day.
Revealing mistake: Right after the scene with the witches, Cindy disguises herself while offering coffee to the producer Corky Shimatzu. However, besides the Groucho Marx glasses and nose, she is wearing her normal outfit when a few minutes earlier, she was wearing her witch outfit, had green makeup on her face, and her hair was a completely different style. Then a few minutes later, she goes back to her play costume. That makeup must have taken at least an hour and would take just as long to remove it. Yet she changes from and back to it in a matter of minutes.
Safety First/Crime Sheen Investigation - S1-E12
Other mistake: During Crime Scene Investigation, Jimmy explains his costume to Carl and, while saying "Sherlock Holmes", his chin goes into his jacket. (00:14:38)
Safety First/Crime Sheen Investigation - S1-E12
Other mistake: When Jimmy dresses up as Sherlock Holmes and says, "Sherlock Holmes," his chin goes through his jacket.
Who Framed Jimmy Neutron?/Flippy - S3-E14
Other mistake: Stormshuckle tells Jimmy he was able to get into his lab using DNA from Jimmy's spit that was left on a straw. Throughout the show, it is shown that Jimmy accesses his lab by scanning a strand of his hair, never his saliva.
Continuity mistake: When Jimmy and Cindy first arrive on the island, Cindy's shoes are grey. But earlier in the episode and later, they are pink. Yes, she was soaked with water from the ocean, but it should've made the pink on her shoes only a darker shade, maybe even red, but not grey. (00:04:59 - 00:16:16)
Lights! Camera! Danger! - S3-E3
Continuity mistake: When Jimmy and his friends are falling from the top of the building, they are all wearing sunglasses. However, before they're about to hit the ground, only Carl has his sunglasses on. When they get back on the roof, they're all wearing sunglasses again. (00:08:43)
Normal Boy/Birth of a Salesman - S1-E3
Other mistake: When all the school kids are meeting outside the school when the meteor approaches, some of the background characters appear twice in the same shot.
The Evil Beneath/Carl Weezer, Boy Genius - S3-E13
Plot hole: In "The Evil Beneath", after Jimmy, Carl, and Sheen escape Dr. Moist's secret lair, they fly back in the hover car where they start seeing some evil fog shadows, and take off. Earlier, being out of fuel was the cause of the hover car's crash landing, but somehow it's been refilled to escape.
Suggested correction: The hover car's crash landing was due to engine failure, not being out of fuel.
Crouching Jimmy, Hidden Sheen - S3-E8
Other mistake: When Sheen is about to fight Yoo Yee, Jimmy puts the kung-fu disk in the dance machine. During the break in the fight, Jimmy asks Cark to get him the kung-fu disk to put in the dance machine, but Jimmy already had it in there at the start of the fight.
Other mistake: After Cindy says yes to Jimmy's proposal, he jumps with excitement until he realises what he did and screams "no" very loudly. Cindy is walking several feet away. How did she not hear him?