Most formula feeds are cow milk based and are equally hard to digest as is cow milk. Milk is just an optional food item and you can remove it from diet and put other nutritive items instead. Give curd or yogurt. Your child basically needs a mashed version of adult diet low on spices.
Although there is a possibility of muddy or greyish stools being linked to jaundice and liver disease, other symptoms like not feeding well and yellowish discoloration of urine and skin are likely to be present along. Unless that is the case, probably it is due to inability to digest the milk properly.

Hi...by what you quote, I perceive that she is otherwise active and growing well. If the only symptom she is having is muddy colored stools, you need not worry. The red flag signs include - yellowish discoloration of the eyes, pale white stools, complete loss of appetite, altered sensorium, constipation. If these are not there, you need not worry.
Regards - Dr. Sumanth