Too much watering can cause loss of nitrogen and consequently yelloying. So then in reality it is not the water per se, but its action, taking nitrogen away with it. With the seedlings make very weak solution, about 1/4th normal strength, maybe 1/5th. But instead use it insteds of plain water every other time.

I agree that you should get rid of the weeds and fertilize. My Sweet Cherry peppers seemed stunted too. After transplanting, the plants more than doubled their growth and each put out about 3 peppers. Then they seemed to go dormant. For about a month or so, there was no growth and no more buds. My solution was to fertilize weekly with water soluble 10-30-10 fertilizer and every two weeks to give a dose of Epsom salts, either 1 TB sprinkled at the base of each plant, or foliar feeding with a solution of 1 TB of Epsom salts per gallon of water. This treatment really worked and the pepper plants are loaded with new flower buds.

Maybe a little bit overfed/fertilized would be my best educated guess. I'm doing green bell & orange bell this year and have not fed them much at all (a little Miracle Grow water once, maybe twice the whole lifespan). I keep them watered once a day, sometimes once every other day, but they are container plants, so they need more water. The only soil I use is regular potting mix with no additives (manure & such). I doubt pests are your problem. Did you start them from seed? Any pictures? I wouldn't worry too much for the time being until someone on here more knowledgeable gives you advice after posting pictures of them or whatever since you have new green growth. Watch the new growth well to see if it assumes any of the rust spots or the leaves start to discolor. Only other thing I can think of is to back off the Safer 3 in 1 on those plants only & see if that helps.

alrighttype, i just checked every single leaf (I even put my reading glasses on ;-) on my holey pepper plant, and I can't find any worms, or worm frass. HOWEVER, I did find 2 tiny eggs, which look like hornworm eggs. I can't find any worms of any type though. And the tomatoes (wouldn't they be much more tasty to the hornworm?) are 3' away, in full foliage and are not chomped upon. Isn't that strange? I did find one parasitized hornworm on the nearest tomato about 3 weeks ago, but have seen none since (I assume there must be some more if there was one)but so far (knocking on wood) no tomato leaf/plant damage. Anyway, thanks for prompting me to look and for the link. We'll see what develops! Here's the link to the eggs I saw Here is a link that might be useful: Tobacco Hornworm egg