Answer: This late in the season I suspect the culprit is a little green fruit worm. These are difficult to control once they've bored into the fruit. The botanical Bt (sold as Dipel) will control the worms on the plants and keep them fruit ruining the fruit, but there's not much you can do to save the peppers once you find holes in them. Inspect the plants once or twice a day and handpick any of the tiny worms you see, and look for eggs laid near the stem of the peppers. If you see any, hose them off or wipe them off with your fingers.
Best wishes with your peppers!
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