Yes, I'm another novice that is turning pens. I come from a long line of woodworkers, but never had much interest until my 30's. Now I live 4 hours away from my dad, so I have to turn to the Internet for guidance. I have crafted several things from wood, most often rings and picnic tables, but recently got into pen turning as a way of supplementing my income.
On to my issue. I sand in this order: 220/500/1200, then go through all the micro mesh pads. I started noticing dark marks on my pens and thought it might be the micro mesh has surpassed it's life. I started another pen and stopped after the sandpaper. I still see them!
I'm using (gulp) Harbor Freight sandpaper, maybe that's the issue? (Remember the income supplement? Harbor Freight is cheap). I'm willing to upgrade sandpaper, if need be. Maybe it's both the sandpaper and worn out micro mesh?
Dark spots in question: http://imgur.com/a/jBxpNGL