I've never had a problem. Since I mist neem every day, I mix it kinda weak. So you can really control the dosing... spray, allow to dry, see where you're at. After about a week of daily treatment is when I started to see the leaves shining.

And I don't spray any plants until they have 2 sets of 'real' leaves. Clones should be totally fine. Neem is a really mild product. I think in India it's used to treat fungal infections like Athlete's foot!