Yes, donepezil can cause GI problems. Talk to his doctor.
Yes, I think stomach upset can be a side effect. Have decreased the dosage for my Alz husband, and seems to be improvement.
Can’t say I’ve heard of donepezil causing leaky bowels but I can tell you that, when my husband got to the point, where he was put on the antipsychotic Haldol (for agressive agitation), he became incontinent.