Some owners of cars with shaker hoods have experienced a fading or loss of paint where the shaker seal comes into contact with the underside of the hood. Besides cleaning the underside of your hood frequently, to prevent the gasket sticking to the paint, you may want to install mylar protective film. The clear decal is not very expensive, at $19.25, and is good protection for your ride. 14-16 Dodge Challenger Shaker Hood Proctection Clear Decal Kit Mylar Mopar OEM SWMDECALSHAKER | Steve White Parts
I could see that happening from the seal rubbing the clear coat off. Darn good suggestion to put some protective film on the bottom side of the hood.