Bump i noticed your question is sliding down the page even though no one has answered you yet. Maybe some knowledgeable person will come along. In the meantime there's always the pepper forum.

Helen, how far way are they from the lights? If you are misting them and they are too close my guess is they could be burning. Another possibility is the water may be too cold and causing water spotting but without a picture it is hard to say. Are these plants small plants or mature plants? Mature plants that are getting old will do what irina says. On small plants it could be too much water or too much fertilizer and the build up is causing the stunting. Fertilizer build up is unlikely but it would not hurt to flush the pot with clear water and give the plants clear water for 2 weeks then resume with fertilizer at 1/4 rate each time you water. Every 4th watering with plain water to leach the soil so the fertilizer doesn't build up. It would really help to see a picture of a plant showing the symptoms you are describing. These are only guesses as what possibly could be wrong on my part. The Violet Barn is a great resource on how to grow. Go to violetbarn.com and look on the home page for the cultural section. You could email them and see what they suggest as well. Dave

It is just one form of stress on the plant. Many times it is from shock from rapid temp changes from cool nights. Otherwise if it is inside then it could be leaf edema from too much water. Plants inside rarely need water, even if it is root bound.

Update: Mystery solved! I came back home from a trip a week ago, and found the tree had dropped a third of its leaves. On closer inspection I noticed spider mites on the top of many of the remaining leaves. I’ve had spider mites on multiple plants before and usually catch them early as I see the tiny red dots and clean them off. Weeks ago when the yellow spots first appeared, I had looked very carefully on the whole tree and didn’t see any mites. Even zooming in on the photos above, I can’t see mites, although I can see a little bit of stippling. My guess is that they were at a stage I couldn’t see, or were a different type of spider mite than those I’ve seen before. I took the tree outside and treated it with insecticidal soap. This time when it was wet, many tiny webs became visible in the branches - it was heavily infested. I wasn’t sure if the spider mites had infested the tree after it became sick with the mystery yellow spot disease, but on Wednesday I got an email from the agent at the Florida agricultural extension that had responded before, saying she thinks the issue is spider mites! - She had just seen a presentation where the yellow spots were shown as a spider mite symptom, although an unusual one. I really appreciated her following up. It has been a learning experience - I now know that I can’t rely on visual inspection for spider mites, and that if yellow spots appear on a plant, it is a good idea to treat it with neem or insecticidal soap to be safe. I’ve treated my other trees and will repeat treatments on this key lime every few weeks until I’m sure they are eradicated. Hopefully it will survive - it produced a great crop this year. Thanks everyone for your help - and John, thank you for your suggestion of checking for spider mites - I should not have assumed that if I can’t see them, they are not there! Happy holidays!