Ascended Fanon: "Lyoko-Warriors" ("Lyoko-Guerriers" in French) originally was a name give to the protagonists by the French fans. Starting with season 3, the characters in-story started using it as their official name.
Cross-Dressing Voices: Barbara Weber-Scaff as Ulrich and Kiwi, and Sharon Mann as Jérémie — and that's just the main cast.
Early-Bird Cameo: Ulrich, Jérémie, Odd, Yumi, Milly and Kiwi popped up in a short produced a year before Garage Kids called "Les Enfants". The only one with noticeable design differences is Ulrich.
Fan Nickname: One particular week in North America, every episode of Code Lyoko featured XANA targeting Yumi. This became known as the "Pick on Yumi week". Notable in that this term became so expressive, it was even noted on The Other Wiki for awhile!
Keep Circulating the Tapes: Until 2011, only Season 1 and the first five episodes of Season 2 were out on DVD before Funimation quietly dropped the title. (Funnily enough, the Season 2 DVD advertises a further volume that was never released.) Due to the popularity of the series and the rarity of the DVD, it was ultra expensive. So you were pretty much on your own until all four seasons were put out on iTunes in late 2010/early 2011. Eventually (as of December 2011) all four seasons were released on DVD, but considering the last airing of the show was 4 years prior, it was a long wait for many fans.
Eight episodes — including the last seven — wound up not making broadcast and were shown only on Cartoon Network's online video service. Executive Meddling is suspected.
In the Cartoon Network run, a major plot element was left unexplained because of a missing episode. "Lab Rat" was the episode where Jérémie developed the technology to translate the Lyoko Warriors' avatars into the physical world, but it was never officially shown for reasons only known to the people at CN. Thus, as far as the viewers were concerned, Ulrich and Yumi teleporting into XANA's factory looked like a complete Ass Pull.
No Export for You: Only two of the CL novels have been released in French, the show's mother tongue, and they were in no language but Italian for a year and a half. An English release will likely never occur.
Although Matthew Geczy is most remembered as Odd's English voice actor, he was voiced by Christophe Caballero in the episodes "Teddygozilla" and "Log Book".
Although Jodi Forrest is most remembered as Sissi's English voice actress, she was voiced by Christine Flowers in earlier episodes.
This also occurs when different voice actors voice the same background character between episodes. For instance, Barbara Weber-Schaff, Mirabelle Kirkland, Sharon Mann, and Jodi Forrest have all voiced Heidi Klinger.
Screwed by the Network: At the end of the fourth season, Cartoon Network, with no reason given, dropped the show, leaving eight episodes to be killed off on their horrible online video service. They then gave the show a brief 6 AM slot for reruns a few months later before killing it off entirely. And it got them good ratings. A Cartoon Network executive confirmed on his Twitter that he personally disliked the show.
All of the voices are done by seven people, each of whom has one main role and then several minor roles (with the exception of Paul Bandey, who is only Franz Hopper). Jérémie and Aelita are the same person, for one. So are Jim and William. Sharon Mann, as both Jérémie and Aelita, is not just talking to herself, she's romancing herself!
All background characters are quite noticeably major characters with a slightly different inflection. The only exceptions are Ben of the Subdigitals, who is voiced by Noam Kaniel (who also sings the theme song), and a purported background cameo in "The Secret" by three fans who visited the studio during recording.
Throw It In: In the episode "Tidal Wave", Odd's final line, "I'm so hungry!", was ad-libbed by his dub actor.