Yep I noticed it on the lower section as well, but I suspect it was due to the pants I had been wearing with press studs on the rear pockets and them scuffing up the material. I make sure if I wear those pants I make sure the flap is covering the studs. . I need clean the "fluffing" off as it increases the wear rate.
Would be interesting to see if Skoda would replace it under warranty..... let us know how you go.