Cut some CSM into little 1/4 inch peices. Mix it with resin and hardener. Stuff it in the holes. They small enough it be fine. Sand it flat enough to tickle you.
Use a gel coat repair kit they sell here on Iboats. I used on one mine they are great. Look online google pigment mixing or color mixing in painting. Same thing they teach how to do it. You can get it close just practice with a tiny amount.
I put it on my boat with a bondo squeegie. If if the consistency of toothpaste. Sand and buff. I never put any surface agent like wax. It works fine.