During her time in Sakura's body, Kira began to notice that certain people were aware of her presence. Kiba and Akamaru were able to smell her, Neji and Hinata could detect her faint chakra signature with their Byakugan, and then there was Kakashi. For some reason, whenever Kira was out in the moonlight and Kakashi happened to be around, he would see her. This led to him asking Sakura questions about this mysterious girl. It was only when Kira got her own body in Shippuden did everyone learn the truth.