The way to fix any imperfections in paint, IF you are sure it has enough paint on it, is to work backwards from the finest, or least aggressive method, to the coarser ones. When I paint a car, I want to perfect the finish. I start with 800 or 1000 grit wet sanding the car. Next I go to 1500, then 2000. I might even do a Trizac cut with 3000 on a DA. Next step is to use a compound with the proper pad (either firm foam, or wool). Next is a liquid polish ( like Meguire's #2, or 3m 205). Use a lambswool, or soft foam pad for that. Then comes a swirl remover or glaze (Meguires's # 9, or Race glaze, or 3M hand glaze) This can be done with a super soft foam pad, or by hand. Final step is a good, non-abrasive carnauba wax to protect the paint.
So to fix your problem, if wax doesn't do it, try a swirl remover, if not, go to a liquid polish, and so on, until you are satisfied. Just be aware, the more aggressive you go, the more paint you are removing!