2011 Car - Body Rust?

Is anyone familiar with diagnosing if a car has rust coming through the paint? My wife has a 2011 Mitsubishi Outlander Sport and it has a bunch of little orangish/greenish specks all over. I tried claybaring it, but I can't get the spots off. I am starting to think it may be rust coming through the paint. Anyone ever have this issue before? I was going to wax the car today, but if I can't get these spots off, I don't want to waste my time waxing it in the case I bring it to the dealership. The shop isn't open on the weekend, so I'd have to take the day off to bring it during the week.

The car has been washed every 2-3 weeks since purchase with a carnauba based wash and wax.