I've seen that happen when the soil is TOO moist, without enough drainage, and when the air is too dry. Also, if the soil pH is even a little off, clones with spankin' new root systems seem a lot more susceptible to that. Finally, if there is a lot of nitrogen in the soil, or none at all, you can have issues.
I would try to do the hardening-off more slowly. Try a completely inert, undertilized soil like seedling mix or promix. During the hardening-off period, after the clones have fully rooted, I like to mist them LGIHTLY when I first take the dome off with a mixture of SMC leaf wash and GH Micro to help them start feeding and growing, while protecting them from dry air. Don't give them too much light too soon either. If you can find a dome that has adjustable vents, those are GREAT, just leave the vents open, or prop the dome up so there's a crack around the base just SLIGHTLY to get them used to drier and drier air.

You wanna hear something silly, I have been putting newly-rooted clones into my hydro table on a PERFORATED nursery flat with the dome over, sitting in small pots of hydroton. I never would have thought they would do so well but I had to go away for a weekend and was like, well, they would die anyway so I might as well test this... lol it works nice. But that's if you're hydro.