I have seen this with a couple of the treeless saddles behind the weightbearing area. Whereabouts is it rubbing on your horse - is it beyond where the bars end? Beyond where the skirts end? Is your horse very flat across the topline or more curvy? Does the saddle extend to beyond the last rib? If the binding is not out of the way properly that can indeed cause problems on certain shaped horses. Also, if the wool is not 100% wool this can heat up and cause hair to be rubbed away.
Hope you get it sorted soon.