Big-Lipped Alligator Moment: At one point in one episode, the Sourceror picks up and eats a worm crawling along his desk. He's never shown doing anything similar at any other point in the series, and it doesn't offer any insight into his character, so one wonders why the show thought we needed to see that except to just be gross.
Four teenagers (whose dialogue is 90% Stock Phrases) are recruited because of their video game skills, to venture into cyberspace and stop a seedy hacker in a Hacker Cave (whose dialogue is 90% Stock Phrases and who has no (apparent) motivation) from causing chaos on both the internet and the real world. Probably intentional, since this format was the only way the producers could sell a ReBoot reboot to investors.
Tre deserves an entry all on his own. In a tech-heavy setting, the African-American character is a basketball Scholarship Student with an overbearing father who's constantly pushing him to better himself instead of slack off? And that, despite being shorter than Austin in the real world, his Guardian form is twice as large as the others and has noticeably gorilla-like proportions?
Fanon Discontinuity: Pretty much every fan is writing off Guardian Code due to its heavy departure from the original show.
Just Here for Godzilla: Due to his fairly faithful characterization and Timothy Brummand doing an admirable Tony Jay impression, some people watch the show primarily for Megabyte. Hexadecimal's presence also perked some people up.
When Parker steps out of the bathroom in an early episode, he lingers in front of the door long enough for the viewer to reaaally take in the giant sign stating "GENDER NEUTRAL BATHROOM" in enormous letters hanging conspicuously over his shoulder. Regardless of one's opinion on the matter, it was very ham-handedly staged.
Whether intentional or not, the ReBoot fanboy from "Mainframe Mayhem" crying "After twenty years, Mainframe is back!" comes off as less of a tribute to old-school fans and more of a Take That, Audience! due to how much of a stereotypical basement dweller he is.
When Bob first appears in "Mainframe Mayhem", he almost immediately begins reciting his Opening Narration monologue from the original show's intro. It's incredibly awkward.
The Scrappy: While most of the human characters are rather divisive, people seem to generally hate the Sourcerer, primarily for being the main villain over Megabyte, but also because his reasons for being evil are vague to almost non-existent.
Sequelitis: Fans of the original series find that this one has a significant drop in quality.
Serial Numbers Filed Off: For all the comparisons to Code Lyoko and Superhuman Samurai Syber-Squad, the show that The Guardian Code bears the most resemblance to is MP4Force, a 2006 animated series about four teenagers that get recruited by an online game and get transported to a secret room where they upload themselves to cyberspace to prevent a virus and a human causing problems in the real world. Yes, it's literally the exact same premise. Worth mentioning that MP4orce was produced by Michael Hefferon, CEO of Rainmaker Entertainment, and creator of The Guardian Code.
The first Netflix "season" of The Guardian Code, which comprises the first ten episodes of the full twenty-episode season. Although Megabyte is a main villain, every other returning character is stuffed into the last episode and returned to their original 1994 configuration, implying Mainframe has been literally rebooted and the four original seasons have been undone. Hex's redemption and sacrifice, Matrix & AndrAIa, Megabyte becoming a Trojan horse and hijacking the principal office; all these major plot points/character arcs are dropped.
Some fans of the original feel this way about the idea of a hacker Big Bad, which could be a legitimately dangerous or interesting for the Mainframe to face... And it's completely wasted on a Cliché Storm that might as well have nothing to do with the original series.
Hell, the idea that us Users have become aware of the beings living inside our computers has so much potential in itself— especially when we would learn that we've been inadvertently killing the residents simply by playing games for fun.
One episode has the Sourceror using an attack by Megabyte as a distraction so he can break into a tech corporation's office and steal a secret prototype computer system. Ample opportunity to provide backstory for the Sourceror (Did he used to work for this company, and the computer is his design they stole from him and now he wants revenge?), but ultimately the prototype only exists as a plot device to make the Sourcerer impossible to track in subsequent episodes and nothing else about the episode is ever revisited.
Took the Bad Film Seriously: As mentioned above, Timothy E. Brummond's spot-on performance of Megabyte is commonly cited as one of the show's few saving graces.
Uncanny Valley: V.E.R.A. once she gains a human body. Being a computer program, her attempts to act human are very off.
Unexpected Character: Hexademical returns as a villain, despite turning good and then dying in the original show.