It's hard for me to judge the state of the wormholes from the pictures.
If the edges are clean and no darker than the surrounding wood, then I would agree with Kenny and use sanding dust mixed with CA or epoxy. Frankly, my experience has been better using epoxy for filling voids compared with CA, but others may have different experiences.
But my experience is also that holes like that are often also discolored a bit, and using sanding dust can creates donut-like circles. So in those cases, I prefer coffee grounds and epoxy. A light-colored infill will only accentuate any discoloration that may exist, while the discoloration won't be noticeable next to something really dark like coffee grounds.