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.
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