No real easy fix. If you do it as you described, you need to be careful to not sand a low in the panel. Also it can be risky filling a pinhole when in anything but filler or epoxy. I've seen filler in pinholes that were filled late in the process let go after the paint is shot.
Have no idea idea of your process or what you used so I'll give you the safe way to do it. Sand lightly with 320 dry or 400 wet. Don't go crazy. Find something that fits into the pinholes. Like a sewing pin or similar. Scratch the inside of the pinhole. Blow off apply 2 part glaze thinly pressing down. Swipe it in two directions to ensure the pinhole gets filled. Sand and apply either 2k urethane or epoxy and sand with 320 dry or 400 wet. You do not want to apply the primer thick, just enough to fill the sanding you did. Then either spot seal the area or base directly over. If the color is metallic finish with 600.
Hope that makes sense.