Not tuning your waxing iron is a common mistake amongst many waxers and tuners who are just getting started. A smooth iron sole plate is very important as you don't want to impart too much scratching on the ski base. It is also very important to have a proper base bevel and a deburred base edge prior to waxing. An edge high base will scratch the sole plate of the iron, then that will lead to scratches on the base. Minor scratches are nothing to worry about, but still, you don't need to make matters worse. Minor scratches should never be repaired other than scraping to remove the high spots as any base repair creates more crystalline areas where wax can no longer be "absorbed" into the sintered base. Avoid any base repair unless it is a significant gouge.