Protection from Editors: The books editors changed often, the first was Seuil, then Flammarion. Now they've moved to XO. The reason was, Seuil's editors helped to fix the text of the first book before it was edited for the first time. Judging from the success that followed, it was maybe not a bad thing. But Sophie Audouin-Mamikonian later called them "idiots" for that. She moved the books to Flammarion, faced the same problem, then came to XO where her texts are now published without any correction (including republishing the first books as they were originally written). And that's not for the best according to some readers as there are now grammatical errors, overly long chapters and overly short ones, etc. SAM in general has the reputation of hating any and all criticism leveled her way and refusing to take it.
Romantic Plot Tumor : Starting with book 8, even Magister has forgotten his initial goal of world domination in favor of courting Selena. It's gotten to the point that we never even find out his secret identity... But the reader is told everything about the fair amount of beta couples (Sparrow and Fabrice, Fafnir and Sylver, Mara and Archangel, Chem and Charm, Lisbeth and Various, Xandiar and Séné, Betty and a werewolf (and later Jar), Jeremy and Sanhexia, just to name a few).
Sylver and Fafnir. The two had had only a handful of conversations about their shared dwarven heritage when suddenly a device in which dwarves are bonded to their one true love similarly to Twilight's infamous imprinting method is brought up. Sylver isn't even a dwarf and shouldn't even be subject to this, but this is Handwaved as it still working on him due to being raised by them. The two kiss, are bonded to each other, and from then on are treated as a perfect couple with no on-screen setup whatsoever.
Arguably Tara and Cal. While the two were good friends, Tara had a longstanding relationship with Robin and Cal was in love with a woman named Eleanor, then flirted with Mara, Tara's younger sister. While Robin and Tara had a rocky relationship, Tara rejected many other suitors in favour of Robin in the past. Come the 8th book, suddenly Cal falls for Tara and Tara dumps her boyfriend to be with him with little prior buildup to this.
Villain Decay: Magister was initially an imposing villain aiming to take over the world. His goal of being with Selena was secondary to his villainous ones. Gradually he became much more obsessed with Selena, to the point where he throws away his perfect opportunity at ruling permanently in the tenth book in favor of being strung along and stalled by Selena acting like a Bridezilla to distract him.
YMMV from the animated series:
Anvilicious: You would think Tara would stop being over-protective of Fabrice since the entire cast seems to have a constant urge to tell her to do so every five seconds. Ironically, it doubles as a Broken Aesop, since the episode's conflict could have been avoided if Tara was more involved.
about the Seasonal Rot from the 8th book on and the waning believable "awesomeness" of the heroine. It seems like all new projects of adaptations are abandoned now—live action adaptations, notably.