The lighter green, yellowish ones could be overwatered. Also, the plants look long and leggy which could mean that they were reaching for the sun. Did you have drainage holes in the bottom of the cups? I do not know what the mold or fungus is, but I have seen it before. Sorry.
This is what I know about tomatoes: They like to be planted deep, and the pic of the one with the cups lined up behind it needs to go way deeper.
They need watered early am and I see that you have drip irrigation so that is good. No water on the leaves that way. I use coffee grinds for the first planting as a good nitrogen aid, but I wouldn't fertilize any more right now. I have rain barrels and I try to water with the rainwater because it has nitrogen in it and is a good boost to quick growth, but as I stated before they are good for quite a while on fertilizer. The store bought one has blooms! Wonderful, because that is hope. Good luck to you and plant those others deep. You will see a difference.