Stop spraying! The fly is irrelevant and spraying chemicals on tiny seedlings is going to damage them. Especially when you don't know what you are treating for. I can't see what you refer to as black fungus. You say you put them out in the sun. Did you harden them off first? ie. Introduce them very slowly and carefully to the outdoors? Also what is the mix they are growing in? It looks very chunky for seed sowing. Other reasons for failure are overwatering and not having drainage in the cups.

But...but...but... it's only baking soda! Is it bad for seedlings? I read somewhere that they use baking soda spray for gnats and other tiny insects.

Re the black fungus, my camera can't show it very well but in the last photo, the tiny leaf is black on one side. I'm thinking of separating them from the rest of the healthy seedlings.

I hardened them the past few days although yesterday, we had a lot of rain so I wasn't able to take them out. Maybe it wasn't as gradual as I thought? Because I left them out the whole day today.

The medium is compost with dried rice husks. The cups have holes on the bottom and drain fairly well.

It's probably sunburn. You can't just expose plants that were started indoors to direct sun outdoors right away. You have to start with them in full shade outside and then gradually expose them more and more to increasing amounts of sunlight slowly over many days to a week.

This is because indoor growlights or sunlight filtered through glass is much less powerful than UV radiation from direct sunlight. And sprays can aggravate the burning, even sprays made from household products.

@gorbelly That's probably it. I didn't think about the UV rays when I first set them out. I just thought, "Okay I have to put them under full sun". -_-|||
I hope my little plants survive. It didn't help that noonday temp here is like a furnace.