In my case, it was determined to be a paint spray problem - most likely a nozzle-type problem - by the robots that apply the paint at the factory.
As it was explained to me, the entire body parts that receive the paint are all assembled, then the car is sprayed as an entire unit. This apparently assures that all painted body surfaces have the same exact shade, coat, consistency, etc.
One thing I would insist on is that any repair be up to FACTORY specifications and be a precise match for the rest of the car. I filed an official claim with Daimler Chrysler on this and requested that the entire door simply be replaced. That would have actually been the least expensive fix for the Dodge, quickest action, and would have allowed the defect to be sent back to the factory quality personnel to evaluate the exact problem (and take possible preventive action.
The Caliber went to a contracted (a Ford Dealership's) body and paint shop for a week. Came back as a terrible job, with an uneven surface, multiple small "dents" on the door, and massive fine scratches under the clearcoat throughout the repaint area. I told them to merely replace the door.
After more corporation/dealership determination, they offered to try another repair/repaint at a different place. It went to another (GM dealership's) body and paint shop, and came back as acceptable - after THREE WEEKS in the shop.
I accepted this repair under one condition - if at any time, this repaired area fades, wears, or otherwise changes condition in a way inconsistent with the rest of the Caliber - it will be "strike three" as far as "Lemon Law" statutes and I will initiate such action pro-rated to that vehicle use and value.
A few other recommendations - be sure to insist on a no-cost and acceptable loaner vehicle during any repairs for such a FACTORY defect. They may not give you any hassle about that - but it is just the right thing for them to do. I had loaners both times - although they would have been provided anyway as I bought the extended warranty with the car's purchase.
There may be a few other points to include about this - but I can't think very straight at the moment because of jet lag and sleep deprivation. No matter what, make sure you get it reported and documented with your dealership and that it is addressed at the corporate and factory levels because it is obviously a MANUFACTURING defect.