Fractured glass.

Take a Sharpe pen and dab the black on the marks on the dark wood. Or (better job) art stores sell all colors of alcohol based markers and with fine tips. Get Dark brown and dab the white spots on dark wood. Live with the fractured glass on the light wood. The alcohol based marker will not bother epoxy.

Banging glass is one of the downfalls of strip building construction especially glass over soft wood.
On boats that have been totally finished, I mix artist oil paint and match the wood and varnish over it once dry.

Once your final fill coats harden, it won't happen that easily.