You can also mix saw dust with clear shellac to the desired consistncy (depending on the problem) and fill the hole or crack. After it is dry , give the whole project a coat of shellac as a sealer and lightly sand the surface before finishing.
I usually make it about like toothpast or thicker. Just be careful with the over coat because it will soffen the patch shellac and smear or come out if you brush or wipe it too hard.
It will be some what darker than the surrounding area but, not nearly as noticable as some glues (Titebond for example) will be. You can still finish the project how ever you want. Stain, paint or polyurethane and the only one that will ever see the problem area it is you.
Rog