Arc Fatigue: There were many who felt the final battle between Melissa and Cerise dragged on too long and grew tired of the constant tug-of-war between them. Which was compounded by the comic suffering from constant Schedule Slips.
Base-Breaking Character: Applies to Cerise and Faith, with the latter frequently being the subject of heated debate on the comic's official forum.
Made worse when the series ended with Mel letting her literally get away with attempted murder. You can imagine how well that went with some of the readers.
In Faith's case, there were those who liked her and accepted that she wasn't without her faults - while others refused to acknowledge the change she made and continued to see the worst in everything she did.
Harsher in Hindsight: Cerise's throw away line, here (about an incident involving a volcano), doesn't seem as funny after she she claims to have killed Jacqui and the student council by teleporting them into one.
Moral Event Horizon: Cerise crossed it in chapter 15, by exposing Mel and Jacqui as witches while they were surrounded by the student council. Then tried to kill all of them, by teleporting them into a volcano, which included the girl she'd been pretending to date in order to gain popularity. And was too busy toasting her success to care.
There was also speculation about whether Faith was mind-controlling the students at Artemis, in order to seduce them; causing some to question whether any of her trysts could be considered consensual. It was eventually revealed that her powers had sync'd with the school, due to her subconscious desire to be loved. But since she hadn't beenaware of it, many readers felt it couldn't be rightly held against her.
Too Bleak, Stopped Caring: Some readers didn't care who won between Melissa and Cerise during vol.4's final chapter, since both are shallow, petty, and manipulative. Melissa was simply the lesser of two evils, by virtue of being the protagonist and because of the wand's influence.
Skye had a genuine crush on Cerise, but was only used by her to make Callista jealous. When Cerise and Callista hooked up, she tried to be happy for them, but failed and ran off in tears. Even Cerise felt a bit sorry for her.