E = SmallGroup(32,28) is the first example.  It has two central subgroups A1 and A2 isomorphic to A ≅ 2 with quotient isomorphic to SmallGroup(16,11), but A1 and A2 are not conjugate in Aut(E).

Examples such as this are reasonably common in p-groups.

**Edit:** You can even have such an example with G abelian: G = 4×2, A = 4×2, E = SmallGroup(64,3) = 8⋉8, Z(E) = 4×4. E has two central copies of A=4×2 that are not conjugate in Aut(G), but the quotients are both abelian and isomorphic to G.