Continuity mistake: When everyone is inside the Museum, Carl offers a Cherry Flavored Fruit Chewy to Cindy. She jumps at it and takes a bite, then clears a stain on her lips with a handkerchief, which she then drops. Carl bends down and picks it up, and then Cindy jumps with a boost from Carl. But in the next shot of Carl, he doesn't have Cindy's handkerchief.
Suggested correction: Carl doesn't bend down to pick up the handkerchief, he bends down so Cindy can use his back to jump off from.
Other mistake: In the episode with the Lake Monster, Miss Fowl and Sam get attacked, the Lake Monster crushes the boat, but when Cindy shows the slideshow the picture shows that they are getting rescued standing on a complete boat.
Factual error: Jimmy consistently says he needs to extract the mitochondria from a virus to cure everyone. In actual biology virus' have no mitochondria or other complex molecules within them.
Audio problem: In the episode where the Wheezers obtain super powers, at the end of the episode, they are all singing their "Sitting and Singing" song surrounding the flaming duck. When the camera cuts to Carl putting his glasses on, the song can still be heard, but everyone's mouth just keeps saying "Standing, and standing, and standing," even though there are more words heard than just that.
Other mistake: According to "Attack of the Twonkies", if music is played around them, they'll mutate into a monster. However, in "My Big Fat Spy" during the song "I Have The Ring", there is a twonkie in the room that is somehow unaffected by the music.