I generally use a bit of sanding dust with water and a few drops of glue added to make a stiff putty. Smear it in with a putty knife, let it dry and do the final sanding.

If you are worried about glue or epoxy staining, use masking tape around the spot and peel the tape immediately after applying the fill. This works well for an epoxy and sanding dust mix.

Alternately if you using epoxy and sanding dust, do the filling immediately before laying on the glass and wetting out the glass. I've done this when I missed a spot and find it just before glassing. Combine it with masking tape for insurance.

If you want to make a gap between strips completely disappear, the sanding dust and wood filler solutions will be somewhat visible, try carving a deeper groove using a V-groove gouge that carves a 90° groove about 1/16" wide tapering away to nothing at each end. Then cut a 1/8" or 1/16" square strip of matching wood. Press a corner of this strip into the groove with some glue. Hold it down with some tight masking tape. When the glue dries remove the tape and plane the excess strip flat.