Take $C = BG$ for some group $G$ and take $D = \text{Set}$. A functor $BG \to \text{Set}$ is a $G$-set. Two $G$-sets are unnaturally isomorphic iff they have the same cardinality, and it's easy to find two $G$-sets of the same cardinality which are not isomorphic as $G$-sets, e.g. find a group with two non-conjugate subgroups of the same index.