Huh. Looks like some kind of surface contamination around the seams causing poor adhesion. That's a bitch. Certainly doesn't look to be caused by rust. (Sidenote: the pre-facelift base model Fiesta hoods had rust and water retention issues right at the front of the hood, on the inside of the seam, because the water drainage ports were completely occluded by the rubber weather seal. AMAZING JOB FORD!
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Since it is under the hood, and your car is a very dark color, I would recommend the following
if you cannot get it repaired under warranty:
1. GENTLY remove all loose paint under the hood around those seams. Carefully use a plastic scraper to do so. Be careful not to remove paint on and over the edges!
2. Use 200-300 grit sandpaper and alcohol to gently clean up the bare metal areas.
3. Use a small brush to apply at least two coats of POR-15 paint to the bare areas.
POR-15 will adhere to, neutralize, and prevent rust. It shouldn't stick out too much on your car, and from the look of it you'd only see it when your hood is open anyway. A can large enough for this job shouldn't cost very much. A 4oz may work, and is about $14 on Amazon right now.
Alternatively, you can get a quote from a local body shop... Though at that point it would probably be cheaper to buy a new, primered hood for them to paint, for as much as the labor would cost you to strip and prep your existing one...
In any case, good luck with your fix. I'm sorry you're going through that - looks like you got the factory paintshop B-Team's handiwork.
Definitely check the seams on your other closures - doors, hatch, etc. I hope it's just contained to your hood and was caused by it being improperly prepped before spray or something...