Just removed the bubbles from the seams of my (2000 f150) doors all along the bottom. Happened to my mustangs once they were a year or so old as well. (Now I'm a keener on oil spraying the doors when new, and every 6 months)
Strip 'em down with a power wire brush etc, use a rust converter before painting (don't get it on the good paint), paint, clearcoat, wait , rustcheck or other oil undercoat sprayed in doors and drain holes.
Apparently when the machine bends the metal at the seam, the protective coatings crack or chip. Just add water - Let the rust begin!
It's off to the seam on the tailgate now - what a drag.......