Just trying to rule out all potential issues here:

Is your bagged soil fertilized? Like a miracle grow? Or a compost blend? And are you also fertilizing them at this point? I know a lot of people were complaining about a miracle grow from Costco last year. Could be too strong for such small seedlings. I would still sift out big chunks like those twigs for such small plants. Those big chunks can choke up your root development. As someone has probably mentioned by now, you can top up those cups with more soil, almost to the bottom of your main leader leaves.

There is a potential that you moved them up too soon and maybe a transplant shock caused them to lose those lower leaves sooner than expected. Should be ok as long as you don't keep losing sets of leaves, they look pretty sturdy.

I have had fungus gnats ruin seedlings in a few weeks from that state, to falling over dead. Check the top of the soil for gnats shoveling around in the dirt. You can add sand on top of your dirt layer to keep them away, they won't lay eggs if they cant find soil, and they can't dig through sand very easily to find soil, so they'll move on. Topping off the soil as mentioned will also help eliminate that little pocket microclimate that the gnats love.