I seem to remember reading, I think in Ted Moores book "Canoe Craft" that you do not attempt to fill the holes as the capilary action of the epoxy into the staple holes will fill them. If you try to fill them with a thickened mixture, it will stop of the hole and cause the capilary action not to work. On the first coat of epoxy with the glass covering, you have to watch the staple holes as they will suck the epoxy from the glass. The inside coat will not act the same as the holes will already have been filled.

Now what to do? I would drill them again, maybe put some glass patches on the inside and wet it out, the epoxy will suck through the hole so keep adding a little epoxy until it begins to harden enough to quit running through the hole. When hard, sand the outside and inside patch, walla, all fixed!