We have graphic novels in the library where I work and they all go to adult non-fiction just to be on the safe side. We are just beginning to add these to our collection and are trying to keep on the lighter side of the genre - like Superman, Batman, and Justice League.
This needs to be called to the attention of the library director. It could have been an honest mistake. A lot of libraries have standing order plans and just get whatever the publishers think are the popular titles. We have a plan like that but I always check the graphic novels before we put them out because like you said too many people think they are all for kids because it's a comic.