A normal subgroup is invariant through all inner automorphisms of the original group.
A characteristic subgroup is invariant through all automorphisms, period (inner or outer) of the original group.
An example of a normal but non-characteristic subgroup can be found in the multiplicative Quaternion group $Q$: The subgroup $\{1, -1, i, -i\}$ is normal, but not characteristic. By defining a "re-labelling" automorphism of $Q$ that swaps $i$ with $j$ (and $-i$ with $-j$, of course) we see that is obviously isomorphic to $\{1, -1, j, -j\}$, even though conjugation by no element of the group can achieve this mapping (i.e., it is an outer automorphism).
Is this always the case? In other words, which one of the following is true?
A) If a group $G$ contains a characteristic subgroup $H$, it can not contain any other subgroup different but isomorphic to $H$ ("only one copy").
B) A group $G$ might contain several different subgroups $H, H', H''...$, all isomorphic to each other, but still lack any automorphisms (inner or outer) that map the H between themselves.
It seems to me that the "re-labelling" used to generate the necessary outer automorphism in the Quaternion example (and thus prove the group non-characteristic) should always be achievable, but I am not confident of this.
EDIT: Thanks everyone for the feedback. Now I see how short-sighted my question is: A group $G$ can potentially have many subgroups isomorphic to each other (e.g., several "copies" of $C_2$), perhaps some of them characteristic, without said isomorphisms necessarily extending to an automorphism of $G$.

Consider the dihedral group of order 8. Its center has order 2 and is characteristic, but it also contains other subgroups of order 2. There are plenty of other examples.