Unfortunately, I can't specify the specific APIs and metabolites I've encountered ultrasonic degradation, but last year some retinoid drugs and metabolites showed degradation that was avoided by simple shaking of the volumetric..
I tend to avoid using ultrasonics for "at risk" compounds.  As ultrasonication is effective because of the high localised energy, it would not be easy to separate out the effects of heating, especially as aqueous solvent misxtures can quickly transfer heat away 
If you want specific published examples, you may have to go back to the 1960s and 1970s when ultrasonics were being considered. 
" Ultrasonic degradation of aspirin in mixed solvent systems "
T. E. Needham Jr., Robert J. Gerraughty 
J. Pharmaceutical Science v58 p62-64 ( 1968 )
Abstract 
The effect of ultrasonic energy on the degradation of aspirin in ethanol-water, diethyl ether-water, and diethylene glycol-water solvent systems at various concentrations and temperatures was studied. It was found that the application of ultrasound to a system undergoing degradation would cause an increase in the rate, but would maintain the same kinetic order as in the control system. The heat of activation seems to be lowered by the mechanical vibrations of the ultrasonic energy. It is postulated that the ultrasonic vibration increases molecular collisions and the movement of the products away from each other, thereby producing a change in the overall rate of reaction. As the concentration ratio was increased in the diethylene glycol system, the subsequent increase in viscosity had a damping effect on the ultrasonic vibration. 
I should note that many of the baths/probes from that era were much lower energy that current multiple-transducer ultrasonication systems. 
Or you could look at the issue with automated sample preparation...
Automated Sonication and Sample Degradation; A Study of Two
Pharmaceutical Formulations.  Peter J. Doyle
AstraZeneca Pharmaceutical & Analytical R&D
http://www.jasco.hu/konyvtar/Prelude-Ap ... n-AP13.pdf
As far as I'm aware, the plan to use ultrasonic compression to speed up the manufacture of pharmaceutical tablets hasn't been implemented which may partly be due to staility/degradation concerns.  
I'm sure a WWW search would reveal many specific examples of ultrasonic degradation of chemicals, as it was proposed as a means of cleaning up process effluents and destroying toxins. 
As I noted earlier, it is the analyst's responsibility to ensure that the sample preparation does not introduce artifacts.
Bruce Hamilton