The challenge is that the theory has to remain effective. You are asking about adding new axioms in stages. For the first few stages things are clear. We can make $F_2 = F + G_1$, $F_3 = F_2 + G_2$, etc.
So we can make the theory $F + \{ G_i : i \in\mathbb{N}\}$. Let's call that $F_\omega$. That will be an effective theory as well. This means that, just from $F$, we can enumerate the entire sequence of formulas $\{G_i : i \in \mathbb{N}\}$.
So we can then continue, making $F_{\omega + 1} = F_{\omega} + G_{\omega}$, $F_{\omega + 2} = F_{\omega+ 1} + G_{\omega+1}$, etc.
Eventually, we can make $F_{\omega + \omega}$ in the same way. To do this, we need to enumerate the entire sequence of formulas $\{G_\alpha: \alpha < \omega + \omega\}$, but we can do that effectively by enumerating $\{G_i : i \in \mathbb{N}\}$, then $G_\omega$, then $\{G_{\omega + i} : i \in \mathbb{N}\}$. So, as long as we have a good grasp of the overall sequence of extensions we have made, we can enumerate the necessary sequence of Goedel sentences.
For the incompleteness theorem to apply, we need the theory at hand to be effective. The problem, as you can see, is that we have to have a computable way to keep track of the "stages", so that we know which sentences have been added at each stage. There are limits to how many stages can be described in a coherent, computable way. The stages are usually treated as ordinals, re-using a concept from set theory.
Essentially, in order to create the Goedel sentence $G_\alpha$ for some ordinal $\alpha$, we need to have an effective way of describing $\alpha$. Recall that the Goedel sentence for a theory refers to an effective axiomatization of the theory, and to axiomatize one of the theories in our sequence of extensions, we need to know just how much it has been extended.
The easiest limit on how long we can keep going is that the number of stages can be at most countable, especially when the theory at hand is only countable. If there are only countably many sentences overall, then we can't continue adding Goedel sentences an uncountable number of times.
It turns out, however, that if we want the description of the stages to be effective, it cannot be near uncountable. The least bound for the computable ordinal numbers, known as the "Church-Kleene ordinal", $\omega_1^{CK}$, is countable. So our sequence of extensions will eventually have to stop, not because we run out of sentences, but because we run out of effective ways to describe the overall sequence of extensions we have made.