Let $(\Omega_1,\Sigma_1,\mu_1)$ and $(\Omega_2,\Sigma_2,\mu_2)$ be two totally finite measure spaces (which implies that $\Sigma_1$ and $\Sigma_2$ are $\sigma$-algebras).
(As usual $\Sigma_1\times\Sigma_2$ will mean the $\sigma$-algebra generated by the set $\{ E \times F \,|\, E \in \Sigma_1 \textrm{ and } F \in \Sigma_2\}$)
Let $A\subseteq \Omega_1\times \Omega_2$ such that:
for almost all $x\in \Omega_1$, $A_x=\{y\in\Omega_2 \,|\, (x,y)\in A \} \in \Sigma_2$ and the function $x \mapsto \mu_2(A_x)$ is $\Sigma_1$-measurable.
for almost all $y\in \Omega_2$, $A^y=\{x\in\Omega_1 \,|\, (x,y)\in A \} \in \Sigma_1$ and the function $y \mapsto \mu_1(A^y)$ is $\Sigma_2$-measurable.
$\int_{\Omega_1} \mu_2(A_x) d\mu_1 = \int_{\Omega_2} \mu_1(A^y) d\mu_2 > 0$
(Note that $A$ is not supposed to be $\Sigma_1\times\Sigma_2$- measurable)
Can we prove that there is $C\subseteq A$ such that $C$ is $\Sigma_1\times\Sigma_2$- measurable and $\mu_1\times\mu_2(C) > 0$ ?
You can not conclude that. We don't need to use the Continuum Hypothesis to show a counterexample. Here is a simple counterexample.
We will use "countable" to mean "finite or countably infinite".
Given $E \subseteq [0,1]$, we say that $E$ is full if $[0,1]-E$ is countable.
Let $\Sigma$ be the $\sigma$-algebra defined as: $\Sigma=\{ E \subseteq [0,1] \,|\, E$ is countable or full $\}$.
Let $\mu$ be a the measure defined on $\Sigma$ by:
$\mu(E)=0$ if $E$ is countable;
$\mu(E)=1$ if $E$ is full.
Now, let $(\Omega_1,\Sigma_1,\mu_1)=(\Omega_2,\Sigma_2,\mu_2)=([0,1],\Sigma,\mu)$.
Let $A$ be the set $([0,1]\times [0,1]) -\{(x,x) \,|\,x\in [0,1]\}$
It is easy to see that $A$ satisfies the three conditions.
On the other hand, any set $C$ in the $\sigma$-algebra $\Sigma_1\times\Sigma_2$ is in one of the two cases below:
Case 1. $C$ is a countable set of horizontal and / or vertical "lines", each of such "lines" being either full or countable. In this case, $\mu_1\times\mu_2(C)=0$.
Case 2. $C$ is the complement (in $[0,1]\times [0,1]$) of a set in case 1, let us call such set $B$. It is easy to see that $B\cap \{(x,x) \,|\,x\in [0,1]\}$ is countable, so $\{(x,x) \,|\,x\in [0,1]\}\nsubseteq B$ and so we have that $C=[0,1]^2-B \nsubseteq A$.
This shows that there is no $C\subseteq A$ such that $C$ is $\Sigma_1\times\Sigma_2$- measurable and $\mu_1\times\mu_2(C)>0$.