Too much light on the clones. If they are trying to grow LEAVES, they won't be growing ROOTS, and they will lose a lot of moisture through transpiration.

Stem trauma- it'll heal; keep your humidity down so it doesn't rot.
Roots- No biggie. It happens. Roots above the soil will even grow bark eventually. It's the fresh roots that are actively taking up juice that need to stay in the dark at all times.

Read the link in my siggy in regards to cloning tips.