paint chipping on roof, rusting is accruing throughout roof

I bought this 2008 Commander April of last year (2015) with 117,000 miles on it and shortly after noticed that the roof had chips from front to back. I managed to find some paint from the store to cover the really bad spots but I know that under each chip is a rust spot that is only going to get worse if the vehicle is not stripped of the defect and repainted. Has anyone had a similar issue, and have you had any luck getting reimbursement from the manufacturer even without warranty? (I have an extended warranty that does not cover paint.)