I was washing my truck a couple of weeks ago and I noticed very small pin head size rust spots on the surface of my paint. I immediately drove over to the dealership as the truck is a 2004. I was informed that this was known as rail dust. Apparently small metal shavings, filings, etc. can settle on the surface after painting. Fortunately, they have a service bulletin on how to fix this. It affects 1994 to present toyota tacomas. There was no charge for the cleaning process they used to remove these spots. I would suggest checking out your vehicles and taking them into to get looked at if you have "rail dust"
2004 Tacoma Double Cab, 3.4L V6 Auto, White, non TRD