Filiform Corrosion/spider rust
 

April 2014 Mazda 3 made in Japan. Defects.
About 5-6 areas of spider like filaments on the roof with pinhead openings where it has rusted underneath and pushed up the paint to it's weakest point at the head. Definitely too small for stone chips. Is this common on 3-4 year old cars? Also a few other very small spots with rough surfaces with very very fine lines like crazy cracks? About the size of a match head. Could be a warranty claim? Defects under paint/contamination during manufacturing?
Edit: Sorry I didn't actually realise this was a Subaru site! I think my problem could affect all makes.

I would get the professional opinion of a body work man and ask him to provide you a report if he feels it is a manufacturing defect and then approach the dealer and take it up with them.