I think the first time you see Yin change her spector into human shape is when she saves Hei from being lost in the black abyss at the end of Episode 25 season 1. I think this is the first time she really acted on her emotions and free will even as a doll, and therefore evolved beyond what a doll is. I think this added to the fact that she was also within the gate. It could also be that Bai powers somehow rearranged her molecular to something more than a doll.
