Why does my ferret have granular, dark stools despite medication?

Thank you for using Petco Pet Education Center, formerly Petcoach! In my experience, granular stool in ferrets is caused either by feeding a diet with bones or by an issue with the way the food is digested. The dark tarry stools can also be caused by certain foods or digested blood or bile. Bleeding in the intestinal tract can be caused by certain parasites or ulcers, both of which are fairly common in ferrets. Both of the medications prescribed are used to treat both conditions - metronidazole is an antiparasitic medication with some antibiotic properties, while omeprazole decreases acid production in the stomach.
You may want to re-evaluate the diet you are feeding your ferrets, and ask your vet about running some tests to check for blood in the stool as well as to check how well the intestinal tract is digesting food. An abdominal ultrasound can be performed to see if there are any ulcers or masses present. I hope this helps!