Gender Queer was never intended for children. It is aimed at adults and young adults.
The NEA recommended it on a list of books for educators and some people misinterpreted this (perhaps purposely, since it acts as really nice fuel for the fear fire) as being recommended for children.
It is not, nor was it ever, a children’s book. And should not be in a children’s section. At the youngest, it could be in the YA section (depending on a local library’s discretion).