Looks like it got under the seam sealer. You'll have to chip that off to get to the really flakey rust underneath it. Rustoleum Rusty Metal Primer is cheap and very effective. Corroseal is another good option.
I had something similar on a 93 Toyota pick up. Turned out it was just a rust stain, try some rubbing/polishing compound before you get after it with a grinder/sandpaper.
Then you still need to see where it is coming from, if it is just a stain.