I Have the same issue with my 2008 the door hinge paint has bubbled and peeled and it has also started on the hood hinges. It has been that way for quite some time. It is not a rust issue, there is no rust even after they peeled. I think they changed the hinges to aluminum and the paint just peels from them. My brother's 2010 is just starting to bubble. Not peeling yet.
Happy to be trading it in on Thursday and not have to look at the ugly peeled paint any longer. They did not say anything about it and it did not seem to affect the trade in value, as they gave me more than I expected for it. My guess is that it is a common issue on all wrangler around this year.
2015 JK Sahara X
2008 JK, 2004 TJ, 1994 YJ, 1992 YJ, Wrangler Sport