I had some staples break off on my first build. I used the finest nail set I had, and set the broken staple below the surface of the planking. I filled these very small holes with a mixture of wood glue and cedar dust, with just a drop or two of water to get it to peanut butter consistency. Finished the outside of the hull. Fairing, Sanding, Glassing, etc. When I pulled it off the forms to flip it over, I loosened the forms that still had staples stuck in them from the strong back, and flipped the hull with these forms still in place. I kept track of which forms still had staples. I was mostly stapleless on my build, but still used a few here and there. I was able to easily pull the staple stubs through from the inside with a needle nose pliers.
Beginner: I'm certainly no expert, with exactly one canoe under my belt. If you haven't already looked at the Lightweight Solo Tripper Build by Cruiser, I HIGHLY recommend you check it out. I read it, and re-read it. I still missed some really good advice on my first (and only) build.