That looks like you've got porosity beneath your gelcoat surface and you're sanding into it, then the compound gets into the porosity and it becomes visible. 

Hi I have sanded the pattern down up to 2000 grit. Then machine polished, but when polishing it making the surface worse with loads of small pin hole type bits. Iv tried slowing the polisher down. Any ideas? Or should I be hand polishing. I want it to look like glass when I Finnished