MY 2006 BF Mk2 Falcon ute also has a paint problem. I noticed it about four months after buying it new, but was told not to worry. One spot on the passenger side doorsill now has rust starting to bubble and I'm wondering what is underneath. I feel I am being fobbed off by Ford and am still awaiting a reply after getting a quote and photos taken for them.
KEEP the pressure on your dealer and Ford to fix this before it spreads and, you are right to be concerned about what lies beneath the paint that hasn't yet surfaced. The letter below suggests paint quality is shoddy.
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