Squeak Knights - Squeaky Floor Silencing

Silent Floor Solutions fixed the squeaky old hardwood floors in our 2nd floor hall and bedroom. To do this they drill many tiny holes. One year later, I can see all the holes - they are darker than the surrounding wood. You have to look closely and probably wouldn't notice if you weren't looking for them. I'm not sure what could have been done differently to avoid this.
Apart from this, the floors don't squeak, and the work was done promptly and professionally.