Bunk trailers are great, they spread the load of the boat over a larger area of hull. This prevents pinpoint pressure that rollers can cause. But bunks can spread something else. Blisters.  Depending on the quality of the boat, and how often it is used, water trapped in the carpet between  the hull and bunks can leave a blister line where they contact. Easy fix: Pull the carpet off the bunks, drill holes in a diagonal pattern down the boards.
A 3/8 drill bit is perfect. Space the holes about 4 in. apart. Being careful to only staple the sides or bottom of the bunks, restaple you carpet back on and your'e set. . This will allow the carpet to dry much quicker, keeping those blisters at bay.