In my years working on boats I have yet to see any cut up section of hull or deck, unless made using vacuum bagging or SCRIMP, that does not have some voids. I will go so far as to say that I know of no builder, who hand lays a hull or deck, where having no voids is even 100% possible. Many builders also use thickened resin or "deck putty", as they often refer to it as, on the back side of the hull or deck skin to lay the balsa into during lay up. If this begins to kick, or the balsa in not padded down enough, there will be voids. Voids lead to channeling of epoxy, or water for that matter.
Why do I bring this up? I took this photo to show what is happening when you fill a hole with epoxy and come back 5 minutes later to find it has "settled". In reality the epoxy has not in fact settled, unless the tape failed, but rather it has channeled into the voids in the balsa or deck putty. If this happens to you you'll need to wait about 30 minutes then mix up another batch to re-fill or top off the holes. Don't let the epoxy cure entirely or you'll need to remove the amine blush and this can be a royal pain in a small hole.