There are fungi spores on almost everything in nature including plants. Temperatures and humidity in the right combination will cause them to grow. Perfect conditions can make them grow rapidly. If you’ve removed the major affected areas and they are now in a dry cool drying room it should stop...
Horrible growing season in the Midwest this year also. Outdoors also and on the first sight of rot I’ll give them a peroxide solution spray down. If it appears again and in more than one cola the girl is hanging. I’ve seen bud rot infect half of the plant in 24 hours. I harvest with about 1/4...