Have an appt next Friday at the dealer and their paint guy will be there to look at the spots. I washed and clay bar-ed it today as I was going to ceramic coat the rest of it and leave that area until after they looked at it. I was inspecting everything closely before getting started and I kept finding more and more spots. Nothing was really visibly in normal light at normal distance but putting a flashlight on it I was finding all kinds of things. Including some kind of white stuff buried in some of the plastic trim that I couldn't clean off.
So in the end I opted to hold off on ceramic coating until after they look at it next week.

They just have him do a polish on the whole thing and then I can ceramic coat it. If they don't though I'll probably look into getting a polisher so I can do it before ceramic coating it. Not sure where all these spots came from, if it was the factory or something else, but definitely some paint quality issues....
Oh I had the same issue with the gas door too, paint wasn't thick enough on it so it looks brownish in spots under light.