As mentioned, its just an imperfection. Nothing you can do about it now but enjoy it. Most briar will have some imperfections. Some so tiny you can barely see them others so huge you can hardly use the wood for a tamper. Many methods of covering them up, some can be hid by stain,sandblasting,rustication and yours, a putty fill. Staining it won't help as the putty will take the stain differently than the wood. It may look good for a short while but over time, the wood will color differently than the putty.