Goof (continuity error): The number of skateboards and the presence/absence of Jeremy's scooter at the school end of the sewer often conflicts with the number of team members already at the factory. One of the worst examples is in Episode 6: "Cruel Dilemma". Jeremy calls Yumi while riding his scooter toward the factory but later, when Odd arrives at the school end of the sewer, Jeremy's scooter is still there with all the skateboards.
Goof (continuity error): In Episode #1 ("TeddyGodzilla"), Jim is shown putting a padlock on the garden shed door. Immediately afterward, the edge of the door is in plain view. There is a mortise lock in the door, but neither a padlock nor any device used with a padlock (i.e. latch, hasp and staple, chain, etc.) is to be seen anywhere on the door.
Goof (continuity error): In Episode #1 ("TeddyGodzilla"), Sissy applies a mudpack to her face before she is attacked in her room. She is still wearing it at the beginning of the attack, but she is not wearing it when she falls to the floor. After the attack, when she is walking with the principal to the infirmary, she is wearing the mudpack again.
Goof (continuity error): In Episode 5, "Big Bug", Odd is wearing his usual purple and black pants and yellow shoes when he enters the empty study hall with Jim and Kiwi. However, when Kiwi lies down beside the desk where Odd is seated, Odd is wearing the reddish-brown pants and pink shoes that Sissy always wears.
Goof (audio/visual unsynchronized): The time it takes for the Scyphozoa to steal Aelita's memories in the second season of the Code: Lyoko progressively changes throughout episodes, and conflicts with the storyboard. A clear example of this is shown in "The Key", where the Scyphozoa manages to steal Aelita's memory seconds after it captures her. This conflicts with the previous episodes, where several minutes would pass and the Scyphozoa would still not have obtained Aelita's memories.