Brad, is it possible that some surface contamination got on the wood before the glass and epoxy were applied? Or perhaps the fiberglass cloth itself was not clean? In any case, I'd consider stripping off the glass in that area, cleaning it thoroughly, and applying a large patch.

I'd use a heat gun with caution to loosen the glass. Even a hair dryer on high would lprobably work. Carefully make a slit through the glass with a knife after heating a small area slowly. It will peel off from there quite easily, with not very much heat being applied as you go. You can grip the hot glass with pliers, or even a glove.

Clean the bare wood thoroughly with lots of denatured alcohol on CLEAN paper towels. Sand everything smooth. Overlap the new patch on the feathered edge of the old glass an inch or two all the way around. Fill the weave, let fully cure, sand the overlapped edges of the patch fair.

After everything has been sanded and varnished, no one will see a difference. Good luck.

I should have mentioned that after you strip the glass, the wood will still be coated with epoxy. I would use a sharp scraper to carefully remove as much material as possible, right down to bare wood. Sanding can also be done, but you run the risk of grinding any possible contaminants deeper into the wood. When you're sure you have bare wood, do the thorough cleaning with denatured alcohol.

I feel your pain.  CLC often puts stickers marking part identification on materials which becomes apparent only after fiberglassing.  Your cleaning may have also spread the contamination.  Even the tape which holds the fiberglass in a roll is a problem.  

When you cleaned the part, you may have spread the contaminants.  I found the fiberglass roll which was bound by tape did not appear until epoxy was applied.  

The stains become apparent only after glassing.   It will be necessary to sand to raw wood and clean with denatured alcohol and reglass.  I used Dacron materials to provide fairing on the stained areas.  See link for method to make feathered area after repair.

photostream

Regards,

Chenango Pete