For some reason, new pipe smokers seem to worry a lot about unburnt tobacco, called dottle. As you become more adept at smoking a pipe, you'll have less dottle, occasionally none. Meantime, don't worry about it. It's drenched in the dregs of ash and moisture and isn't worth recycling. Throw it out with the ash, even when there seems like there is a lot.
There is a scene in Sherlock Holmes where he goes through his pipe smoking ash and rescues every bit of unsmoked tobacco. Tobacco was relatively more expensive then, but it still wasn't worth recycling. Sherlock was compulsive. Don't be compulsive.