Massage the back of the shoe. That means to push the area at the back where it is bothering your foot and press it down into the inner part of the shoe (fold it down) and let it go, press it down and let it go back up. Keep doing this for the whole area of the back of the shoe. This will soften up the material so that it won’t rub. In the meantime, put bandaids on the area that is bothering you, particularly when you are going to wear those shoes next Shabbos.