There are a few things that can cause this. If your are misting your dome more then twice a day you will likely have mold & the clones will rot. When you mist the dome you need to spray the dome not the plants, spraying the plants constantly will cause them to get moldy or rot. Poor air circulation in the humidity dome will cause the plants to rot. You need air circulation to build humidity. Most customers will cut a hole in the top of the 6 & 3 inch domes, the 7 inch dome has vents built in. Some customers just prop the dome open a 1/2 inch on one end.