Ok, I have made a female mould using the EC epoxy tooling gelcoat and then a few layers of standard glass fabric with laminating epoxy.  I had a few imperfections in the mould so sanded them out but I've gone through the gel-coat and into the fibers in a few places.  I was wondering what is the best way to repair this?  Is it possible to add some wax to the gelcoat to make it behave like a top coat for example and use that on top of the affected areas? 
Many thanks, lee.

If there's quite a few, its easier and quicker to make a new mould, but if its only a few:

Break off all gelcoat in the affected area.
Sand with 120 grit to get rid of sharp edges in the perimeter of the cavity.
Use some flash tape to create a barrier around the area, leaving a 5mm gap.
Mix up some gelcoat with some silica to get it to peanut butter consistency.
Rub the area with acetone.
Apply a the mixture into the cavity making sure it sits proud slightly.
Use flash tape or a piece of bagging material to cover the mixture, sealing it from the ambient air.
Wait for it to cure.
Rub down with 120 until almost level with the surrounding area.
Rub with 240 followed by 320,400,600,800,1200
If needed polish it.