Yep, I get them too...use super glue to fill em in...just squirt a glob on the crack/pinhole/etc and sand it in with whatever grit you are using at the moment. If I discover a crack @ 120 grit then I fill in and sand in with 120, continuing on down to the grit I finish with. The only thing I don't like is when the crack is on dark colored ironwood, as usually the sawdust/superglue mixture is lighter colored than the surrounding wood, but it really is not that big a deal. The end result is usually un-noticeable.
Good Luck,
Hank Hammond