Asaf Karagila's answer covers the properties of transitive models, and where the argument in the OP breaks down. Let me add to that answer by saying a bit about the situation vis-a-vis a very different type of submodel: elementary submodels. Early on it's quite easy to mix these up, so this seems worthwhile to write out.
Ignore class/set issues for the moment (or replace $V$ with some big enough transitive set like $V_{somethingreallybig}$). By downward Lowenheim-Skolem we can find some countable $M\prec V$. Now we do have the bi-implication $\varphi^M\leftrightarrow\varphi$ in general, and the argument of the OP is now worrying again:
Since $M\models\mathsf{ZFC}$ we have some $a\in M$ such that $M\models$ "$a$ is uncountable."
By elementarity, $a$ is in fact uncountable.
But $M$ is countable. What gives?
The resolution of the above issue is that $a\not\subseteq M$ - which is to say, $M$ must not be transitive. So the argument in the OP really reveals a tension between two conflicting "niceness" notions, namely transitivity and elementarity, and shows that while each individually is compatible with countability we can't have a countable submodel which is both transitive and elementary.
(Note that the argument above is closely related to Skolem's paradox, which was the original appearance of the downward Lowenheim-Skolem theorem in the first place.)
Both transitive and elementary countable submodels of $V$ play important roles in set theory; the above shows that they're really fundamentally different types of objects. That said:
We can always turn an elementary submodel into a transitive submodel via the Mostowski collapse (note that this kills elementarity in general, of course).
That said, transitive elementary submodels of $V$ do exist (under mild hypotheses) - they just have to be really really really really big. In particular, if $M$ is an elementary submodel of $V$ then any ordinal definable in $V$ has to be in $M$, and then by transitivity we get all the smaller ordinals too. And there could be really really big definable ordinals: maybe $\mathsf{GCH}$ fails somewhere but the first point of failure (which is definable) is really big, or your favorite large cardinal property actually shows up (at which point its least instance, which has to be really big, is definable), or so forth. So transitive elementary submodels of $V$ only show up rarely.
More technically, countable elementary submodels do have some weak transitivity properties - in particular, if $M\prec V$ then $\omega_1\cap M$ is closed downwards. This winds up being extremely useful down the road.