It’s hard to see in the photograph but that doesn’t look like mould to me. I think it’s root primordia stimulated into growth by the unnaturally hot, wet conditions. As to how to wean them off the tropical rainforest regime I can’t really help. It’s not the climate citrus usually grow in and you’d need to harden them off gradually to more normal conditions. Also they want to grow. To keep them small you'd need to treat them as bonsai which is quite a fiddly business.

From what I red you did every thing possible wrong. it is a wonder the poor thing is still holding on. Transplant the tree into a 5-1-1 medium, climatize it to the sun and feed the tree with a 5-1-3 or as close a ratio fertilizer.

If you prefer growing the plant that way, at least spray them with pesticide, fungicide etc before you put them back into sealed container. Since you create closed ecosystem, anything from outside that able to grow there will grow, include pathogens.

I'm going to go out on a limb and assume that you were trying to do a terrarium setup with your trees due to a perception of low humidity. For some tropical plants, this would be the case. Citrus are, in fact, subtropical and do just fine in a desert environment, so you don't need a high humidity environment such as you would require for a cocoa tree, for example. If you're concerned about humidity, just use an oversized drip tray, then fill it with rocks or place your pot up on pot feet and let the runoff from watering evaporate on its own. I agree with the other posters on here that you need to remove your trees from the jars, plant them in some well draining mix, and then watch your watering. If you're worried about pests like spidermites just make sure that your plant is on a stand or table elevated above the floor. I might take the tops off the jars for a bit, let them acclimate, then remove them from the jars and do a repot. If you want to keep them small you do that by keeping them in a confined pot and pruning both the top and the roots. Look up bonsai. But small won't give you much in the way of fruit. Otherwise just pot up as necessary, pick your ideal height, and prune off growth that gets above that. But I wouldn't do any of that until you get the hang of caring for your trees.

a year and a half in a SEALED jar.. i find that hard to believe.. and wonder if this post isnt a day early???

and if it is .. good one ...

i dont know what could be in your apartment that is bad for trees.. but ok for you ...???

ken

Ken, I think you might have nailed it. R Roll, rick roll?

Thank you all for your thoughtful and helpful replies. I appreciate the advice. I took the lid off today and will repot.
Yes, they really were in a sealed container for over a year. I couldn’t believe it myself but I’d rather just keep them alive and healthy at this point. I didn’t realize how bad it was for them to be in there; I put them in to keep them separate from the other plants and forgot about them :(
When I realized they were still alive so many months later I was afraid to take them out. Now I know.
Thanks again