Certified GKH Gardening Expert
It sounds like there may be an issue, either with humidity, or with over-watering. Hot peppers are known for being pretty drought tolerant, and can survive well in semi dry climates. Although they do prefer regular watering. They just won't want to be wet for a long time.
I would apply a half strength wettable sulfur to the area to kill off any bacteria floating around, but also to lower the pH of the soil slightly. This will help, both, the peppers, and to provide an environment that the disease won't like.
Here is an article that will help: https://www.gardeningknowhow.com/edible/vegetables/pepper/growing-jalapeno-peppers.htm