I've had this happen, as have other friends of mine. What happened is you put it into jars with too much water still in the buds. Probably 20-30% water still in there, and you should be dropping your buds into jars at about 10% or less. I know it's really hard to tell how much moisture is in the buds, but they should definitely feel very crispy on the outside when you jar them, then in a few hours in the jar they should be back to soft and squishy. You only have 3-5 days to get that moisture that's left way down to around 5% or less, and then finish your cure. If you take too long letting that last moisture cook out of your buds in jars-mold forms, due to moisture.
With your current crop...just do what you've already done, chop away the bad spots and make sure it's completely dried. Hell over dry it rather than try and leave a little moisture, that way you know mold can't form. (no moisture, no mold).
Once your buds are all 100% dry, you won't have any issues with further mold growth. Regarding what might be on there but you can't see...smoke that shit. You won't die unless your smoking massive webs of that stuff, and even then you'd probably be just fine as your just inhaling the burned smoke, not the actual spores.