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: When Jimmy is in his lab, in the shot where the camera zooms into his eye, in the shot just before that shot, notice the digital clock on Jimmy's counter. The seconds part jumps from the 30's to the 40's twice in two different shots.
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)
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.
