My 2006 Mustang GT developed blisters in the paint along the front edge of its hood in 2008. Ford Customer Relations contacted my dealer and the hood was refinished at a cost of $500 paid by the dealer. I was given a $1000 option to replace the hood, including paint, to be paid by the dealer.
The problem is that the aluminum hood does not get properly treated (deoxidized & anodized) to receive paint along its seams. Thus a new hood will have the same problem, so I opted to have the hood treated and refinished by a painter who understood the problem. The refinished hood came out perfect.
A dealer may argue that the warranty is for body rust-through, not blistering of the paint. In this case go to Ford Customer Relations for help. Each dealer has a fund to correct issues related to factory processes, but the dealers are reluctant to spend the money.