your water level was probably a bit too high...it should be 2-3 inches below the jiffy pellet....you want the bubbles from the air stone to create an aeroponic effect. But going forward I wouldn't even use the jiffy pellets. I germinate my seeds in paper towel, then put them in rapid rooters or rock wool, and place them into my homemade aero cloner...it's a small dwc system but I use a big air stone and the bubbling is enough to keep the roots wet and aerated at the same time. I clone using the same method too. Been using this method for 2 yrs now and am still 100% success rate so far. I use a product called Dyna-Grow KLN which is THE BEST rooting product around. It is basically a "liquid" rooting gel and it makes you roots go crazy with growth. Also, if you are two weeks in your plants need some sort of nutrients, I use 1/4 strength until they are growing vigorously then I up the nutes.
The most important thing in DWC is maintaining the roots. Water temp, and bennies like Hydroguard or enzymes like Hygrozyme or Cannazyme will keep your roots healthy and prevent root rot. Or you can go the opposite of the beneficial bacteria route and use Res Clear or UC Roots to sterilize the water killing all the beneficial bacteria but also all the harmful ones too.