It deals very heavily with the heroine's suicidal musings and her various attempts at killing herself.
I must admit that the suicidal stuff scares me partially b/c I went through my own struggles with that in my teens. I don't know that introducing the idea that people struggle like that makes one more likely to do so, but I worry about it none the less.
Apart from the mental illness theme, she also considers her sexuality.
That was exactly what made me shudder when I read The Lovely Bones after dd. She is young. She seems old for her age and she's very centered, but she's not at the point of impending sexuality. The Lovely Bones starts with the rape and murder of the main character. There are also various parts where it discusses the sex life of the main character's parents and her younger sister, who becomes sexually active at 14 after her older sister dies. She, conveniently, stays with and eventually marries that boy and doesn't get pregnant until after they are married.
I'm really not prude, but having my 12 y/o read about sex, sexual violence, and the sexual musings of those older than her is daunting for me.