Later in the movie, Coraline’s father calls her a “twichy, witchy girl” while singing to her. Throughout the movie, magical, supernatural things happen around her. However, we later discover that these things are traps meant to lead Coraline to her handler. All of these scenes allude to the witchcraft aspect involved in MK programming.
At one point, Wybie gives Coraline a strange gift: A doll that looks just like her.