DIAGNOSIS You're likely using a cleaner that leaves a residue, or the microfiber cloth itself has picked up oils or dust that it's smearing around. The glass needs to be pristine for good scans.
FIX Here's the shop method. 1) Unplug the printer. 2) Dampen a *lint-free* microfiber cloth (like for glasses or camera lenses) with a little distilled water or isopropyl alcohol. Don't spray directly on the glass. 3) Wipe the glass in one direction with gentle pressure. 4) Immediately dry it with a clean, dry section of a second lint-free cloth. Use a bright light at an angle to check for streaks.
IF THAT DIDN'T WORK If stubborn spots remain, they might be on the underside of the scanner lid or the white backing plate inside the lid. Open the lid and carefully clean those surfaces with the same dry cloth technique.
HEADS UP Never use window cleaner, abrasive pads, or paper towels. The ammonia and other chemicals can damage the anti-glare coating on the glass over time, and paper towels will scratch it.