Rust under the hood

I have a 2006 mustang GT (bought it 3 months ago w/ 28,000 miles and now have 32600). Anyhow, I was changing the oil this weekend and looking under the hood where the edge is rolled there is bubbled up pain consistent with surface rust. My wife has a 2004 ford ranger and has some of that on the bottom of the tailgate (inside).

Has anyone else had this problem and since the car is under warranty should I bring it in?

My other option would be to scrape it off and sand and paint the area.
 
The hood is aluminum. That bubbling is just some sealer material they used because my 07 GT has that same bubbling. I picked up the Stang about 1-2 days after it left Flat Rock, MI.