I know that its not really a Subaru but my wifes 05 92x has a couple of spots on the roof where the paint is flaking off. Its black and kept outside but I keep it clean and this happened fairly quickly .
Still under warranty right? Take that shit back!! If you do it now you may get the paint redone for free.
It should be covered under the body warranty (36k for Subarus, not sure if they upped it for the luxury "Saabarus").