The submitted photo images does not clearly show the damage symptoms that you are describing.  But I am suspecting you are seeing symptoms of oedema (or edema). This is a physiological phenomenon that occurs when the conditions result in the stomatal cell closing but the plant is still taking up water.  This results in pressure build up in the plant cells and causing it to rupture.  This unsightly symptoms is not one that can be removed.
Also formation of adventitious roots is not uncommon in succulents.  However, I am curious that if the plant in your photos is an Echeveria, your plant is in poor health with the elongated internodes (probably due to low light environments).  It is not clear from the photos, but could your plant be a Kalanchoe?