Hey Bizzy,
It looks like you have some fungal issues. Fungus gnats can be a vector for multiple pathogens (as well as eating your roots) but many plant pathogens are endemic, and will colonize your plants whenever environmental conditions permit.
Clone domes are convenient, but they limit air movement, and high humidity and stagnant air can foster pathogen development.
I would recommend soaking your plugs in a bioprotectant like Root Shield to suppress pathogen development. Increasing airflow by opening your vents sooner and removing the dome more often will help as well.
For larger grows, I don't use domes, but build cloning chambers where humidity, temps, and airflow can be managed.
I hope this helps.