either you took the cuts wrong and they were damaged, you have somehow hooked the bubbler up incorrectly or the water is tainted(algae for instance). really the only things it could be. but what kinda answer you looking for with one sentance to describe your problem... i mean lets be real it practically paints a picture...
I've had clones live in the bubbler for two months before they started to grow roots..as long as the leaves stay green up on top and not wilting....patience is a big requirement for cloning sometimes..not all plants are easy to clone..some are resistant to rooting..lazy buggers..I find turning the lights lower and not letting the water touch the stems helps make them reach with their roots..there needs to be a lot of bubbles though..in a 2 gallon tub..I use two long air stones..the little bubbles pop all around the whole surface..if you make a big closer you will have to add more air stones..whatever you do...don't mist the clones..just keep the humidity dome on until the roots get about an inch...then slowly adjust more lighting and allow them to have some fresh air for a hour each day..once new growth happens pull off the dome and go full cfl over them..as you would with a seedling...after that about two weeks and they ready for planting in soil.