When Vicky is in the house with Sarah, and sees the drawing that Sarah has made, the Children come to sieze Vicky. As the Children drag Vicky out of the room, it is clearly evident that she has no shoes on. Later, when she is put up on the cross by the Blue Man, she is wearing her shoes.
Perhaps when they were dragging her out of the room, her shoes fell off. And then when they noticed that she had no shoes, they decided to put them back on her.