I am not aware of disease that can cause an ammonia odor in the stool.
The most common ammonia-related disease is with chronic kidney disease leading it an ammonia-like breath smell. Sometimes urine that sits for awhile can smell like ammonia - thus any possible fistula (i.e. abnormal connection) between the bowels and urinary system can possibly lead to stools smelling like ammonia.
Another consideration may be fetor hepaticus - a distinctive, sweel breath smell that is associated with severe liver disease. Again, I cannot make a connection with the stool.
Followup with your personal physician is essential.
This answer is not intended as and does not substitute for medical advice - the information presented is for patient education only. Please see your personal physician for further evaluation of your individual case.