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.
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.
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.
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.