Fill holes with West Systems epoxy mixed with 406. Let it kick and re drill the hole.
Note: make sure to wet out wood first with resin to avoid a dry joint.
If its in a varnished peice or its a repair that will be visable when done, mix in saw dust to color the repair. If you can mix in saw dust from part you are working on the match is usualy very good. Still visable though.
I do this like everyday on some boat related project, give me a tough one!