Yup any flaps that overlap with the fender/rocker will cause damage or result in discoloration, even if you use ppf under them. Its just the nature of these things when combined with dust dirt sand etc that gets under them and mechanically rubs against the paint.
This is why if you're going to install spalsh/mud flaps, best to get ones that dont hug the body and stay flush in the fender/wheel wells.