First of all, for arbitrary modules $M, N$ you don't need to have that $M\times N$ is a free module, so $M\times N$ cannot be the free module generated by something. But also if $M, N$ were free, these two modules would not be equal.
I take the following definition: $F_\mathbb{Z}(M\times N)$ is the free module with basis the set $M\times N$. (If you have another definition, comment and I should be able to prove equivalence.) This means that we forget the module structure of $M\times N$ and just make it into a free basis of a module, so for example we have:
$$[0]+[0]=2\cdot [0]\neq [0]$$
where the elements in brackets denote the basis elements.
So for example we have $F_\mathbb{Z}(0\times 0)=F_\mathbb{Z}(0)\cong \mathbb{Z}$. And some non-product examples: $F_\mathbb{Z}(\mathbb{Z}/2)\cong \mathbb{Z}^2$ and $F_\mathbb{Z}(\mathbb{Z})\cong \mathbb{Z}[X, X^{-1}]$ (by the map $[n]\mapsto X^n$).