Pinholes and other inclusions are an endless source of irritation when committed to a bedding job that looks nice.
If your stock is synthetic one option is to use a small diameter drill and poke a hole completely through the stock. Fill a syringe with bedding compound and then inject the hole till the stuff "poops out".
This is about the only way you ensure the void is completely filled. Let it run out a bit, wipe it clean, then finish with installing the action in the stock (coated with release of course) and give it a final squish.
Things to pay attention to:
Make sure you sterilize the surrounding area with a dose of release agent so that the bedding compound doesn't work its way between.
There's no fix (that I've found anyway) that completely blends the buggers. My std practice these days is to scrap the job and start over if there's a hole.