Odd is the most affected when attacked by the Spectre in "Spectromania" (the others get sick; he gets deaf) and the one who has the most difficulty using the Tower. The end of the episode reveals he is the one who lost the most source-code.
As much as the poor quality of XANA's attacks can be blamed on shoddy execution, he really can't do a lot of the more flashy attacks he used before because killing the heroes is not an option anymore.
As pointed by the actors themselves in an interview, Sissi did mention in an original series episode that she dreamed to be blonde. Assuming she just dyed her hair, the change then makes sense.
William is the first to got to Laura after the return to the past doesn't work on her. Well, the same shtick happened to him months ago.
A rather obvious one, but the first hint that the ninjas aren't Xana's mooks (as the Lyoko Warriors and the audience probably thought at first) is the fact that they lack the Eye of Xana.
Why does Odd have brown hair instead of having his trademark blonde hair from the cartoon? Well, beside the fact the actor himself wasn't blonde, it was shown in the previous series that both of Odd's parents were brunettes, which means he could be originally brunette but simply chose to dye his hair, which would also explain his purple streak. He might have simply decided to keep the purple streak but not dye the rest of his hair, lazy as he is.
When the Skidbladnir was destroyed by the Kolossus in season 4 of Code Lyoko, it was said it would take months to reprogram it. Jérémie successfully reprograms it in episode 2, and it seems highly unlikely he remade it during the timeskip when the supercomputer wasn't even active.
In the finale episode, it's revealed Tyron is now married to Anthéa, meaning he is Aelita's legal guardian. The problem is, Aelita technically is around 24 years old, and as such should not need any guardian in the eyes of the law. Her Aelita Stones identity legally is 14 years old, but that identity has her being Odd's cousin, and as such isn't related to Anthéa or Franz in any way. Moreover, no character seems to notice a girl who should be 24 years old still looks like 14 years old, something that was actually mentioned in the original series!
Of the more supposedly mundane variety but Jeremie's ultimate treatment of Laura smacks horribly of user-type bullying (where, through various methods, the bully manipulates the victim into doing "favors" for them) and the rest of the team goes along with it. Never mind that Jeremie's behavior in the original series heavily hinted that people did the same thing to him and that if anyone tried that on Jeremie or Aelita, Ulrich, Odd and Yumi would murder them; the series presents this behavior as perfectly acceptable. No amount of "they're teenagers; they do stupid/cruel things" justification explains away Jeremie turning himself and his friends into the type of people who made him miserable.