Looking at you picture again they look like dust motes. You can see the donut shape and they are out focus since the scanner is focusing on the coin. Put a piece of aluminum foil and scan it. If they appear in the image you found your issue. You need to clean your scanner.
I just tried scanning a piece of aluminum foil but the green/blue spots don't show up. I tried scanning the coin multiple times in different parts of the scanner but the spots on the coin remain on the same place on the coin. So the spots are on the coin itself and not the scanner glass.