Try molding your leather in a plastic bag, I don't know how exactly you are "Pre-molding" your holsters, but I have found if I put my leather in a bag, or under a sheet of plastic/ vinyl or something that it doesn't leave a tool mark. It sounds like what is happening is when the rubber is stretching around your leather on the mold, that it is expanding, and when it contracts it is grabbing the leather. Using a thin smooth plastic layer should take out the direct rubbing, kinda like washers or moleskin.