I also have this on Habs somtimes, usually late in the season. I think it's caused by a fungus already present on the flowers at the time of pollination.

Have you ever been able to get rid of it? It's showing up in all the peppers from my two habs, but not in my ring-of-fire peppers.

I never had so many affected pods that it really bothered me, so never took steps against it. I'm not sure if anything specific can be done. For next season, I'd say don't use these seeds as they'll likely carry the fungus; buy or trade for new stock, grow in pots if possible and use fresh medium, don't over-water and try not to wet the foliage. Overly humid weather conditions could be a factor, but not much can be done if outside.

I have plenty of seeds from a supplier, so I grow new plants, in pots every year with fresh potting soil. The only plants I have in the ground are the superhots I overwintered indoors. They're doing awesome, so I'm just hoping they won't catch whatever it is.

Problem is it's in every pod this year. Haven't had this happen before. I'll give them one more chance with the ones ripening now, but looks like my habs are a write off this year.