First, consider the definition of group isomorphism:
> Given two groups $(G, \otimes)$ and $(H, \odot)$, a group isomorphism from $(G, \otimes)$ to $(H, \odot)$ is a **bijective** function $f : G \to H$ such that for all $u$ and $v$ in $G$ it holds that $f(u \otimes v) = f(u) \odot f(v)$.
Now, consider a homomorphic encryption such as ElGamal cryptosystem: It takes a message from a cyclic group $G$, and outputs a pair $(c_1, c_2) \in G^2$. That is, $\mathcal{E} \colon G \to G^2$.
Notice that under this definition, $\mathcal{E}$ is **not a bijection** from the message space $G$ to the ciphertext space $G^2$. However, the decryption of ElGamal is unique.