Not always. Main thing is to identify the actual source or the mildew smell. Once you figure that out it'll be a lot easier to get Ford to fix it if it's still under warranty.
Spend $5 on Febreze which was formulated to fix odors. I had a mouse nesting and dying in my truck vents and one application of the Febrezee fixed the problem permanently. Even with the windows rolled up and the truck sitting out in the sun the smell did not return.