The conventional wisdom with staple holes is to do nothing. If you have a couple of large brad holes that bother you, take a sliver of the same wood and jam it in (no glue). The problem with putty mixtures is that you contaminate and tint the surrounding area. Then you try to sand the area and create a mess, plus you often create a blemish because the sanding surface doesn't match the rest of the sanded area.
Filling staple holes always leads to mild disaster.