What you have appears to be resin which filled the gap in your wood strip, (after it looked okay and you left for dinner) which later absorbed into the wood in the sides of the gap leaving the resin sucked out of the gaps between the glass cloth weave creating tiny holes.

I agree, this is exactly what it looked like when I get up close.

Unfortunately the physics of surface tension are working against you and you will NEVER fill those holes. Try for a few hours and you will agree. Ask me how I know.

Your choices are to carve them into a groove which you then may be able to fill, or to sand the glass off in those spots and hope a new layer of cloth applied while room temperatures are dropping.

Thanks for the advice. I definitely seem to be struggling a little with the surface tension, I was just hoping there was a trick to getting them to fill. But I've spent enough hours on the build already, a few more trying to come up with a good enough solution won't kill me. Appreciate the help guys!