These dots are due to metal shavings or loose grit from the abrasive reacting with the finish. That´s why it is very important to vacuum clean carefully.
The dots are actually larger than a piece of grit and are almost black in color, no matter what was the color of the original abrasive grit. The finish reacts with the metal present in the grit to form a dark substance. This substance also discolors part of the wood immediately around the piece of grit. If you look at the spot through a magnifying glass, you may be able to see the piece of grit sticking up in the middle surrounded by a ring of color.
The same happens with metal shavings. The shavings can be produced by sharpening a scraper or grinding the metal guard on a sanding machine with the abrasive.
Practical tip: to avoid black dots, vacuum clean carefully. Do not sharpen scrapers in room where you are going to apply finish. Check regularly that the drum of your belt or drum sander is properly adjusted.