In the case of fruit fly larvae, researchers now suspect that the damage is done by a process called acoustic cavitation.
For acoustic cavitation to occur with the short pulses typically used in diagnostic ultrasound, bubbles about 1 micron across must be present in the fluid.
Crum of the University of Mississippi in University, probably produces an enormous amount of acoustic cavitation, which may play a role in destroying the stones and perhaps in damaging nearby tissue.
The nature of the damage indicates that acoustic cavitation rather than a heating effect is responsible for the destruction.
However, such localized effects also mean that acoustic cavitation and its effects would be difficult to detect.