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I started around 120 tomatoes at the beginning of April. When I transplanted them into cups the bottom leaves started to turn yellow and then eventually brown and fall off. Not sure what is going on and was looking for some advice. They have been fertilized twice with miracle grow dissolved in water and I cut it down by 1/4 since it is a 24-8-16 fertilizer. This is my second year starting them from seeds so I am not sure whats wrong with them. I was thinking verticillium wilt, or a nutrient deficiency of some sort.

The rest of the plant looks good. Since they are lower leaves they are more prone to getting splash back and fungal problems, so I would just take off the leaves and be careful not to get the leaves wet or dirty if you can.

Did you only make holes in the bottom of the cups? They might be resting on the holes and not draining properly. Always make holes in the side or cut the bottom corners so hole extends in both bottom and side.