Without assuming the axiom of choice, a countable union of countable sets isn't necessarily countable. In the following proof though, I don't understand when anything that isn't in the axioms of $\sf ZF$ used.
Let $X$ be a countable set of countable sets. Since $X$ is countable it can be ordered: $X = \{G_1, G_2 ,...\}$.
We'll construct a function $F$ that maps each element of $X$ to a bijective function from itself to $\Bbb N$.
Let $f_0 = \emptyset$. We'll recursively define $f_i$: Since $G_{i+1}$ is countable, there exists a bijective function $h :G_{i+1} \to \Bbb N$. Define $$f_{i+1} = f_i \cup \langle G_{i+1}, h\rangle$$ Let $$A = \{f_i \mid i\in\Bbb N \}$$
Since $A$ is a countable set of compatible functions, the set $$F = \bigcup A$$ is a function, with $$Dom(F) = \bigcup \{Dom(f)\mid f\in A\} = X$$
Once $F$ is constructed, creating an injective function $f:\bigcup X \to \Bbb N$ is easy, for example by mapping elements to numbers of the form $2^i3^j$.
I know that the problem with the proof is the construction of $A$, but I don't understand where. When ordering $X$ we chose a bijective function out of infinitely many, so why can't we do the same for $G_{i+1}$?