If you have dusty air, it is possible some of the dust gets inside the scanner and deposits itself on the backside of the glass. If that happens, there's nothing else to do but clean that off.
You have not mentioned what scanner or what object you are scanning. If the object being scanned has a rough surface and there is printing on the OTHER side of the paper, then parts of the other side could show through at spots where the paper is thinnest.