Narm: At one point Morgaine laments the fact that all the men she's fallen in love with have been closely related to her. It's meant to be sad, but comes off less as "Fate has treated me cruelly" and more as "Why can't I stop falling in love with my relatives?"
Overshadowed by Controversy: In 2014, Bradley's daughter went public with the fact that she had been molested by both her parents during her childhood, and she was far from the only one, suddenly putting Bradley in the same company as Roman Polanski and Woody Allen regarding the debate over how much of an artist's own life should impact the judgement of their work.
Harsher in Hindsight: This revelation makes the dynamic between Viviane and Morgaine (especially regarding the Beltane ritual) so much creepier.
Seinfeld Is Unfunny: In regards to feminist treatment of the Arthurian legend. Nowadays, there are a fair amount of retellings from a female perspective (such as Gwenhwyfar and I am Morgan Le Fay), many of which take a less heavy-handed approach than The Mists of Avalon. It's easy to forget how groundbreaking TMoA was, in spite of its flaws.
In the book, while Morgaine is preparing to greet the Horned King, she Sees that the little girl who scattered blood on the fields is being raped by a sinewy old hunter. And Morgaine is apparently cool with this? Oh, and about a page later she realizes she's had sex with her own brother.
Lampshaded when Nimue needs to pass water and is afraid to do it in public. Morgaine is puzzled as to why would anyone want to spy on someone passing water.