I apologize that I need a preamble in which I digress into philosophy, but here it goes:
One of the perceived goals of set-theory is to provide a foundation for mathematics. Natural, rational, real numbers and other structures can be defined inside set-theory. However, students reason about these numbers and structures independently of set-theory. Numbers for example are not naturally perceived as sets, they are atomic, and sets are only needed to collect things. Even in the context of model theory, I feel that I am allowed to work with a model of set-theory, put it aside for a moment, and think about non-set-theoretic objects. They all may coexist independently. I may believe that our "real" sets are sufficiently correctly described by ZFC, so that I believe in the existence of ordinals up to and beyond say $\omega_1$, again alongside other non-set-theoretic atomic objects and structures. I may also have a notion of countable and uncountable collections independent of a concrete set-theoretical framework. Countable collections are enumerable, uncountable are not. This is the key idea of Cantors' diagonalization - there is no exhaustive enumeration of the reals.
End of preamble.
Assume a model of ZFC which is presented as a directed graph: The model universe is the collection of vertices, the element relation is the collection of edges. Vertices are atomic, they are not sets, they represent sets. I choose this representation to avoid distracting concepts around real set membership.
Given such presentation of a model, one can identify some exemplary model-sets. The empty set of the model is represented by the vertex with no inbound edges. The set $\{\emptyset\}$ is represented by the vertex with not inbound edges except the one originating from the empty-set-vertex. And so on.
Define an external mapping $\operatorname{Vert}(s)$ which maps a model-set $s$ to the collection of vertices that represent $s$'s model-elements. Whatever $s$ is, $\operatorname{Vert}(s)$ is a countable collection of vertices, if the model is countable.
Assume we have an ill-founded countable model and want to identify various stages of the constructible universe of that model.
Wikipedia defines: $L_\alpha = \bigcup_{\beta < \alpha} \operatorname{Def} (L_\beta)$
It is not clear to me which ordinals I need to use to construct stages. Is it the "real" ones or the ones the model sees? However, I have an issue with both choices.
Choice 1: Use real (i.e. external) ordinals. I assume that the stages $L_\circ$ satisfy $L_\alpha \subsetneq L_\beta$ for $\alpha < \beta$. If this is so, this should translate to $\operatorname{Vert}(L_\alpha) \subsetneq \operatorname{Vert}(L_\beta)$ for $\alpha < \beta$. Then according to [1], with $\omega_1$ begin externally uncountable, $\operatorname{Vert}(L_{\omega_1})$ should be an uncountable collection of vertices, which is impossible.
Choice 2: Use in-model ordinals. According to [2] there is an infinite reverse path of ordinal-vertices: $\alpha_0 \leftarrow \alpha_1 \leftarrow \alpha_2 \cdots$
How is $L_{\alpha_0}$ even well-defined, when there is no base-case for the recursive definition?
[1] limit of uncountable strictly increasing sequence of sets
[2] Infinite decreasing ordinal chain in ill-founded countable model