The swap-stopper faces are partially protected by a plastic case. The plastic case is slightly raised, to try and help avoid scratches occurring if you accidentally drop the face. This reduces the risk of scratching, and also of the face damaging the inside of the tube.
However, the polished face of zirconium, titanium or silver obviously cannot be covered as it needs to interact with the air-column in the headjoint to have an affect.
Its not the end of the world if you scratch it. Little scratches are inevitable in daily use, and you might find you can't tell any difference in using it.
One way you might accidentally scratch it, is to insert a metal cleaning rod too aggressively. This should be avoided with all stoppers. When swabbing out the headjoint, the cleaning rod should not make contact with the stopper as you could move or damage it.
If you do scratch it and want to repair it, the easiest remedy is to take it to your local flute repair shop, jeweller or engineer. The silver can be re-polished easily. However, the titanium and zirconium need specialist knowledge and equipment to obtain the mirror-like finish with minimal material removal. In addition, all three faces have to be equalised in dimensions to allow you to swap them easily. They are deliberately not totally flat or even - their is a subtle custom curve.
For a small cost, you can ship the face back to me and I will be happy to re-polish it for you.