Without supporting the tarsal joint (that forms the arch) with the orthotics, your bodyweight only goes to the heel, the ball of the foot, and the toe areas. This will hinder the blood circulation in these areas, and in addition to that, will have friction over the shoe bottom as the tarsal joint falls with each step throughout the day. This will eventually cause the callus build-up. Energetic children can build up calluses even at the top of their foot with shoes that cover the whole foot—like sneakers—as the fluctuating arch rubs the ceiling of the shoe.
Treatment: Rid of the root cause of this problem by using the orthotics that align the ankle bones; this will provide even weight distribution throughout the bottom of the foot including the arch area, help the blood circulation, and prevent the friction. File off the callused area and apply some moisturizing cream.