The ammonia smell is caused by putrid water. Putrid water is caused by rotting plant material. Rotting plant material usually means the cuttings weren't oxygenated enough. The vases you had them, because of lack of surface area, in did not allow enough oxygen exchange so oxygen could get to the roots, essentially smothering them. The only way to avoid this is to change the water everyday to keep it oxygenated. Or grow them in a jar with more surface area. Sometimes adding a drop of hydrogen peroxide helps - when added to water, it breaks down into oxygen and water.
Why didn't you plant the cuttings when they grew roots?
