If you have ants put out ant bait. It is hard in a green house in pots to keep diseases and pests from spreading. If you use good sanitation you can keep bugs out of the green house longer but you also keep out the predators. Once bugs get in, it can cause some major issues.
I would move out all of the diseased plants. In fact move every thing out but isolate the plants from healthy plants. Sanitize the green house. I use a 10% bleach solution but I have weed block on the ground. My plants are on benches not directly on the ground. I have a shade house not a green house so air circulation is less of an issue, but bugs can freely enter and leave.
Start at the top and work your way down. Use a nozzle spray and hose every thing down well. I have algae issues so the bleach takes care of that too. Patch the holes that should not be there and make sure the vents and fans are clean and work. Put out ant bait for the ants and if mice are a problem, put out traps for them too. I used to use physan but it is hard to find and a gallon cost $58 but it does last a while. Hydrogen peroxide also works and there are formulations sold at agricultural suppliers that are specifically designed for green houses. It sanitizes for soil pathogens but is safe to use on the plants so you don't have to take every thing out.
Anything that goes back in the green house needs to be healthy and bug free. Dip them to make sure. Anything sick should be in the hospital section somewhere else, or be put out of its' misery.
Plants in the greenhouse should be potted up in sanitized pots (10% bleach solution soak for a week, requires no rinsing. Otherwise I soak overnight and have to scrub and rinse.) Use good potting soil, and water and fertilize as needed. Pot up and out of the greenhouse before the plants get stressed. I have nectar plants and onions planted to attract beneficials and repel pests. In a greenhouse you will need to import the beneficials, but with a shade house I justs have to have the nectar plants in the yard. The beneficial insects can fly into the shadehouse freely.
Peppers do not like soap. You can use a horticultural oil instead and instead of spraying, I find it more effective to mix up 4 tablespoons of horticultural oil in 4 gallons of water in a five gallon bucket and dunk the plants head first in the bucket. Wear gloves and I cover the soil with newspaper or a plastic bag so it does not fall out when I turn the plant upside down. I leave hold the plant in the water for a minute before I take it out.
Black frass can be from the aphids, caterpillars, snails, or slugs. You need to go out early in the morning or after dark with a flashlight to see them. If the peppers are chewed or disappear overnight than slugs and snails can do that and they will go after the fruit. Birds also like to go after peppers especially when they are red.
https://ag.umass.edu/fact-sheets/cleani ... greenhouse