What kind of case u using?? If you using soft material case like tpu well chances are small particular inside your pocket went into the case and get trap between the case and the phone, as time passes the movement be it very slight will cause light scratches to appear on the phone.
It I want it to be clear from scratches, well need to get cases like lunatik, lifeproof or any other that seal off chances of dust getting into the phone like otter series.
Alternative u must take your phone out once in a whole to clear the dust if not use a snap or a hard case which does lot flex and allow dust to get in , also the phone must fit snug to have any chances of slight movement to allow dust to rub against your phone.