Suppose we have a countably infinite set $X$ and we have (countably) infinitely many subsets $A_1,A_2,\cdots\subseteq X$ which are non-empty and distinct (i.e. for any $i\neq j$ either $A_i\setminus A_j$ or $A_j\setminus A_i$ is non-empty). Is it possible (in ZF) to disjoint these sets i.e. come up with sets $B_1,B_2,\cdots\subseteq X$ that are non-empty and pairwise disjoint.
Edit: it is not necessarily the case that $X$ is in bijection with $\omega$ in our model of ZF, we know that $X$ is countably infinite from outside our model.
Since @Asaf Karagila seems to be AWOL, I'll set the misconception in the question straight and answer.
In $\mathsf{ZF}$, any set $X$ has a Hartogs' number $\aleph(X)$ which is the least ordinal $\alpha$ not injectible into $X$. It is always an initial ordinal - i.e. a cardinal.
A set $X$ is called infinite if $\aleph(X)\ge \aleph_0$, Dedekind infinite if $\aleph(X)>\aleph_0$ and infinite Dedekind-finite if $\aleph(X)=\aleph_0$.
If a set $X$ has a collection $\{M_i\}_{i\in\Bbb{N}}$ of non-empty mutually disjoint subsets, I'll refer to this as $X$ having a partition of size $\aleph_0$. Even if the partition covers a proper subset of $X$ it's always possible to complete the partition to cover all $X$ by adding $X\setminus\left(\bigcup_{i\in\Bbb{N}}M_i\right)$ to the partition.
As noted by @Izaak van Dongen in a comment, If $X$ is Dedekind infinite the question is trivial because there is an injection $j\colon\Bbb{N}\to X$ and $\{\{j(n)\}\colon n\in\Bbb{N}\}$ is a partition of size $\aleph_0$.
Theorem (Kuratowski): If $X$ is infinite Dedekind-finite and $\Bbb{N}$ injects into $\mathcal{P}(X)$ then $X$ has a partition of size $\aleph_0$.
Kuratowski's original proof appears in Tarski 'Sur les ensembles finis' (1924). The following proof is due to Halbeisen & Shelah 'Consequences of arithmetic for set theory' (1993).
Define a function $\tau\colon X\to\mathcal{P}(\Bbb{N})$ by $$\tau(x)=\{n\in\Bbb{N}\colon x\in A_n\}$$
This function induces an equivalence relation on $X$ via $x\equiv y\iff \tau(x)=\tau(y)$. The equivalence classes are a partition of $X$ and the cardinality of the partition is the cardinality $|\tau(X)|$.
Claim: The number of equivalence classes is infinite.
Proof: Each $A_n$ is a union of equivalence classes, so if there were only finitely many equivalence classes, there could only be finitely many distinct $A_n$. This contradicts the assumption that the $A_n$ are mutually distinct.
If the number of equivalence classes is Dedekind infinite we can finish the proof as follows - since a Dedekind infinite set has a subset of cardinality $\aleph_0$, we can find a sub-collection of equivalence classes of cardinality $\aleph_0$, and that gives us the desired partition.
The difficulty lies in the possiblity that $\tau(X)$ is also infinite Dedekind-finite.
For $S\subseteq\Bbb{N}$ and $n\in\Bbb{N}$ define $$\operatorname{pred}(S,n)=X\cap\left(\bigcap_{m\in S, m<n}A_m\right)$$
Now define a second function $\chi\colon X\to\mathcal{P}(\Bbb{N})$ by $$\chi(x)=\{n\in\Bbb{N}\colon n\in\tau(x)\land\left(\operatorname{pred}(\tau(x), n)\setminus\operatorname{pred}(\tau(x), n+1)\ne\emptyset\right)\}$$
Claim: For all $x,y\in X$, $\tau(x)=\tau(y)\iff\chi(x)=\chi(y)$.
Proof: Since $\chi$ is defined in terms of $\tau(x),\tau(y)$ and the sets $\{A_n\}_{n\in\Bbb{N}}$, if $\tau(x)=\tau(y)$ then $\chi(x)=\chi(y)$. Conversely, assume $\tau(x)\ne\tau(y)$. Let $n_0$ be the least $n$ on which $\tau(x),\tau(y)$ differ. w.l.o.g assume $n_0\not\in\tau(y), n_0\in\tau(x)$. Notice that $y\in\operatorname{pred}(\tau(y),n_0)=\operatorname{pred}(\tau(x),n_0)$ but $y\not\in\operatorname{pred}(\tau(x),n_0+1)$ because $y\not\in A_{n_0}$ and $n_0\in\tau(x)$. Since $n_0\in\tau(x)$ and $y\in\operatorname{pred}(\tau(x),n_0)\setminus\operatorname{pred}(\tau(x),n_0+1)\ne\emptyset$ it follows that $n_0\in\chi(x)$. OTOH, $n_0\not\in\chi(y)$ because $n_0\not\in\tau(y)$. So $\chi(x)\ne\chi(y)$.
So $\tau, \chi$ induce the same equivalence relation on $X$ and it seems we haven't made any progress.
However, one of the following must be true
Additional references on the subject: Azriel Levy 'the independence of various definitions of finiteness' (1958), John K. Truss 'Classes of Dedekind finite cardinals' (1974), Supakun Panasawatwong 'Dedekind-finite cardinals and model-theoretic structures' (2019).