I bought my F250 SD in Dec of 2018. After putting 4000 miles on it all of a sudden at speeds of 72 to 78 I experienced a vibration like a wind noise. To make a long story short at 18000 miles I discovered the problem. There are two pads made of something like neoprene that are glued on the outside of the cap under the rear window and to see them you have to look between the cap and the bed of the truck. These pads are glued to a ribbed surface and they were coming off and flapping in the wind. Ford says the pads are for sound dampening and to protect the cab in the event that the bed shifts and hits the cap. I took the truck to the dealer who told me that if they replaced the pads they would just come off again. Also they said because I have a sprayed in bed liner they would have to cut off the bolts to get the bed off. So the service manager recommended that I just pull off the pads.
I believe this problem stems from a design flaw. Air traveling down the side of the truck gets funneled between the cab and the bed because the lip of the bed is angled forward. Ford tried to remedy this by putting a C shaped rubber gasket in the space which is flexible. However the gasket allows about 4 inches of space on the top and air can get in thus causing the rubber pad to start to vibrate because as I said they are glued to a ribbed surface and has spaces with no glue or contact. Also the rubber C shaped gaskets are flexible and when enough air pushes I am sure it gets by. The bed needs to be redesigned so that the lip does not funnel air.

I did pull the pads off and the noise is gone but it was a difficult nasty job. You only have about one inch of space to work in and the adhesive they used is a sticky mess that never hardens. So far no other complaints about the truck but this really soured me toward the dealer.
Anyone else out there with this problem?