I wrote this months ago. Take it how you will.
Content on Clare and her former fandom activities is disappearing rapidly, and over the past few months I have alternately searched eagerly for this information and avoided it and any mention of the subject as much as possible.
When I was a freshman in high school, my best friend offered me a copy of Clare's book and said I absolutely had to read it. I knew a little about Clare, but nothing entirely damning. By the time I entered fandom, her exploits had been mostly forgotten, and those who remembered were often silenced by her team of crack lawyers (a team that, oddly, did not involve Heidi8, her famous fandom pitbull lawyer. The divide between these two that has come to light eludes me and my research, although I'm sure there are those more dedicated to searching for it than me).
The most common complaint against Clare is that she is a plagiarist. This is true, and is outlined clearly in a post by a user named Avocado (although journalfen, the site where this is hosted, is currently down, there is a post about this on fanlore). Clare claimed that the quotes from popular shows such as Buffy the Vampire Slayer, Red Dwarf, as well as many others, were just "games" for her fans to find. However, Avocado found damning evidence, and submitted it to the fanfiction site where Clare's Draco Dormiens was hosted. Clare was found guilty of plagiarizing entire scenes from Pamela Dean's The Secret Country. From here, the story becomes much harder to follow, due in part to the loss of many groups and forums where this information was posted. Years later, Avocado posted her story, and details the various accounts Clare and her friends used to hide the plagiarism. For example, Clare claimed that she had written the passages down years before in a writing journal, and later found them and believed they were her own. Avocado was skeptical, and her account is the best place to find information on this subject.
Overall, fandom forgave Clare, and she later was able to get a full book deal out of the Draco Trilogy. Her published series are infamous among many fans for copying scenes almost word from word from her fanfiction, although the plagiarized sections were all cut. Nicely enough, she named this trilogy, the Mortal Instruments, after her Ron and Ginny incest fanfiction (I would link to this, but I'm trying not to get this post taken down immediately. I'm sure you can find it yourself. Also, I hope I never, ever have to see that story again, dear lord). Of course, there were still her bitter detractors--but her loyal fans soon silenced them, and even ran some out of fandom.
But Claire, you ask, why do I care? How on earth does Cassandra Clare's history as a plagiarist and a bully affect me?
I'm glad you asked. In the grand scheme of things, it doesn't. It does not matter. This doesn't affect your life, or mine. The thing is, she hasn't stopped. Plagiarism, sure. I haven't seen any proof of it in her published works--although, that may be because repercussions are far, far worse once you're making money off of something... If you want to read about her bullying, and about how she hasn't stopped, try here or here for relatively recent twitter and tumblr shenanigans. Overall, though, documenting over ten years of Clare and fandom is far, far too much for one blog post--you could almost write a novel about the woman.
Maybe all of this means nothing, and maybe it's too disorganized to follow (and such is the price we pay for so much of fandom history being lost), but I think Clare's story serves as a warning against BNFs (Big Name Fans) and how they can lead to strife and discontent within a fandom. Whether you love Clare or hate her, she's here to stay (and so are all of her stories, easily available online. Yes, even the incest).