Hi
There`s a few things at work here, all fixable. Soil roots need time to convert to hydro. The roots shouldnt be completely submerged as they will suffocate.
Emily`s garden incorporates capillary wicks to bring water/nutes up to the plant which is usually started off in some kind of medium (jiffy plug,,rockwool cube etc). The capillary wicks keep the medium moist until the roots can grow down into the water. The plant will have roots above and below the water line so it wont struggle to breathe.
Transitioning plants from soil to hydro can take a week or more depending on the hydro method used. For example, the transition from soil to flood and drain is less stressful on the plant than soil to dwc.