Sand and re-clear comes to mind. Not sure what is going on there but there's a lot of texture overall as well. Doesn't look like they go all the way down like a real pinhole.
Could be dry overspray that was floating in the air and landed causing a solvent pop effect on the surface, hopefully. A wetsand and buff even on a trial spot will tell if I'm correct.
some light contamination on the surface making the paint lay funny. could have been on the primer before the base or on the base before clear. could also be some solvent pop in the primer making the base look like small dimples when it bridges the pinholes. once you put the clear on its more visible because its glossy