Can be a problem, no doubt. I like to give the surface a shot of hardener before applying the glue. The glue wicks into the faults, but cures rapidly on the surface, minimizing penetration.
Same thing with fills. I use chopped bark a lot, and I like a three-step process. First I use thin to run into unseen cracks, then I like to give a shot of accelerator afterward, put the medium on top, stuffing the ground bark into the void. Glue cures quickly enough to keep the bark or dust from soaking it up and rejecting a subsequent finish.