+xI wouldn't risk using it without filling it to some extent. The void underneath the gelcoat is likely bigger than the pinhole on the surface, so when that fills with resin it will create a mechanical lock that will cause the surrounding gelcoat to break off when you demould the part and cause a much bigger problem.
Filling it with gelcoat should be easy, but you have to make sure that you are actually getting gelcoat into the void. If you are re-exposing the hole after filling it, then it's likely you trapped air in the void that prevented the gelcoat going into the hole. You really have to force the gelcoat into the hole, and use a pin or something to break the surface tension and let any trapped air out.
Otherwise, just use filleting wax. This probably won't be noticeable in the finished part, but you will likely have to redo it every time you use the mould.
Won't be better to make it bigger so gelcoat will get it there better?
But from other hand I have slight concave on that surface and might get flatten after to much sanding in one place.Hmmm