From the picture, it kinda looks like it was clear coated, and the polishing took some of the clear coat off.
The second picture, though, really just look like normal wavy imperfections from the factory. Either way, I'll second Les here, you need to sand with many grits going up to 2000 or 3000. Your starting grit really depends on the depth of the imperfections. I would start with maybe 600, then go up in steps, by the time you get to 1k or 2k, you should see whether or not you got it right. If not, start all over with lower than 600.
You might try just buffing it with a cotton wheel rouge first, though. It's really hard to tell from the pictures.