I think it depends on the depth of the holes, but the general rule of thumb is to expect paint to fill nothing except for pinholes. I don't know that your actual gun spit paint on whatever it is you are spraying, but I think that it sounds like the loss of pressure could have created a sort of orange peel texture? This can happen sometimes when the paint cannot properly atomize. If you can feel something with your hand though, it is likely that another coat of paint will not correct, especially a sprayed coat.

I was spraying an olympic bench press (2 1/2" sq steel tubing). I had primed and sanded to a smooth glass finish and now it feels like sandpaper after spraying paint. I always used oil base paint in the past and now I tried water based. I think I might have to wet sand before I try painting again to correct it. Home depot use to sell a paint called Glitten that was oil base and now its water base...

my new cabinets were started to be painted with Gidden and they are a mess.I have read on this site that it's not the best out there and that SW or BM make a good product is the same $ range.I wish you the best of luck.