Actor Shipping: Quentin×Mélanie, popular even before the actors were known. A bit different from other examples in that they are actually currently dating (and caused quite an uproar when they revealed it!).
Base-Breaking Character: Laura. Some fans are glad a new Lyoko-Warrior finally is joining, others (apart from the Die for Our Ship aspect) are questioning the point of adding a feminine counterpart to Jérémie when such a character (Aelita) already exists, while still others would rather have had Sissi as a new recruit, particularly since she's now blonde and could easily fill a similar role in a much less intelligent (and much less contrived as a result) way. Not helped by "Virus" giving her major Common Mary Sue Traits, and "Mutiny" making her a flat-out traitor.
The 2D being replaced by live-action, of course. Half of the fanbase is excited while the others are crying the death of the series.
The fact two of the Lyoko sectors, Ice and Forest, were suddenly erased for no reason wasn't well-received by some fans. Others seem to be ok with it, thinking it will be properly explained later on. As of the end of the season, it's not explained properly in the show, but interviews with the developers brought to light that they decided to leave out the Ice and Forest sectors so that they can increase the quality of the other projects they adapted for Evolution. In other words, making two really nice sectors instead of four mediocre ones.
Fans are divided about whether Laura being excluded from the group and getting her memory erased at the end of "Mutiny" was a well-deserved punishment or a Hypocrite move from Jeremy, considering how many times he himself ended up putting the Lyoko-Warriors in trouble with his own mistakes.
Die for Our Ship: Laura wasn't well-received by Aelita×Jérémie fans when it was revealed she would serve as The Rival to Aelita. And it only got worst after her introduction episode.
Fanon Discontinuity: It's already been getting a lot of this. That a new creative team is working on it, with the old one only there for the first two transitional episodes, makes it even easier, not to mention said old team's stance on the subject as detailed below.
Informed Wrongness: In "Vendredi 13", William and Ulrich get called out by Yumi and Aelita for acting "dangerous, idiotic and unwise," simply because they decided to pick a fight with a couple of Mantas while the girls deactivated the tower. Aside from the fact that this is a perfectly sound strategy to handle the situation, they weren't even outnumbered and were working well together. The only thing that could be said against them is that they perhaps weren't taking the situation as seriously as they should have been, letting the Mantas strafe them a couple times while doing a Nonchalant Dodge. Yumi and Aelita come off as being overbearing rather than reasonable as a result.
Introducing a spectre in the form of a child who, rather inexplicably, attacks the heroes with easily escapable (literally, they just shove the kid away) yet somehow debilitating hugs. Given, the spectre drains energy from the Warriors by way of skin contact, but it still looks silly. A William spectre does it in the fifth episode, but he was at least strong enough that it took Ulrich's intervention for Yumi to get free, and he later (offscreen) broke down a door.
Even more ridiculous in "Soupçons", where XANA's attack consists in summoning three clones who... stay in front of a door doing nothing to attack the Lyoko Warriors (who are right in front of them) until Aelita deactivates the tower. Even more ridiculous, one of them uses his lightning to repair a stereo, for no apparent reason. In the end this attack ended up helping the Lyoko Warriors more than it hurt them.
Really, almost any attack could count as Narm, considering most of the time they don't do much more than being a nuisance, yet the Lyoko-Warriors react like this was a big deal.
Only the Creator Does It Right / My Real Daddy: The showrunners of Code Lyoko (Jerome Mouscadet, Sophie Decroisette and Bruno Regeste) only contributed to the start of the show and scripted a few random episodes. In a later interview, Decroisette admitted that most of their input into the show was ignored and their work from the series bible of the original show disregarded by the Evolution staff, and as such they don't really feel involved with Evolution and pretty much disown it entirely.
Special Effect Failure: Unfortunately, XANA's attacks on Earth could be more convincing. It's not helped by the fact that the replacement of 2D by live-action forces XANA to give up his usually spectacular supernatural phenomenon (weather control, Attack of the Killer Whatever...) for attacks easier to adapt (spectres).
Take That, Scrappy!: Laura has her memory wiped after betraying the group and essentially gets booted off the main cast.
The 2D being replaced by live-action is the most obvious examples, but it's far from being an isolated case.
Believe it or not, there were fans who were mad the Supercomputer wasn't exactly identical to his animated counterpart (such as reactivating it requiring to connect to cables together instead of drawing a switch).
The new theme song is considered by many fans to be less unique and less likable than the original.
The fact all Lyoko Warriors can now deactivate towers instead of Aelita alone.
The redesign of the Lyoko Towers to look more like something out of TRON still doesn't sit well with some fans.
Several small elements that had to be changed or removed due explicitly to the limitations of the live action: the appearance of the manhole cover note likely constructed so that the actors would have a place to climb into given that those scenes were shot on location, the removal of Kiwi and several other minor characters, the aforementioned Special Effects Failure...
The removal or drastic change in appearance of minor characters — for instance, Sissi and Anthéa are now blonde.
Lampshaded by Ulrich toward Odd in "Spectromania": if he had REALLY been the spectre, he wouldn't have waited so long to take Odd's code. Odd would have made a much smarter choice sticking with him so he wouldn't confuse them instead of leaving him behind. In Odd's defense, though, he was in a state of panic and barely recovering from a previous spectre attack, so his irrational reaction had some justification.
Jérémie in "Virus"; despite being there all day to watch Laura when she is conceiving the virus for them, he fails to notice she has been checking the Return to the Past codes at the same time and modified the virus so it would protect her from it. Keep in mind the previous show portrayed him as a genius who could come up with complex programs, and that he has several years of experience with the supercomputer, while Laura is supposed to have none.
Aelita in "Rendez-Vous". She blindly accepts a message promising her information about her parents if she comes alone to an isolated location when she knows XANA is attacking. When she goes, she finds her mother acting so suspicious she'd have to be shooting lightning to be more blatant. Then Jérémie arrives to get her away from the spectre... and she accuses him of lying, unable to accept the fact it couldn't be her mother. After the spectre is destroyed, she blames Jérémie for it, though she at least realizes how stupid this is by the end of the episode.
Laura gets one when she decides to show the lab to her father just to convince him not to remove her from Kadic. At least Sissi had the excuse of being panicked and worried for Ulrich when she did the same in the original series' prequel. Laura should know they could just use the RTTP to fix things (unless she was paranoid they wouldn't just to be rid of her). Naturally, this result in the Lyoko warriors losing even more of the already limited trust they had in her.
In the same episode, Laura's father is more interested in the supercomputer than he is in the fact that a group of teenagers have access to a nuclear-powered supercomputer. Skewed Priorities, much?