For this, I showed that If we have the set $I=[0,1]$ equipped on one side with the Borel set and Lebesgue measure λ for X and on the other side the same set $I=[0,1]$ equipped with the power set and the counting measure m for Y.
The diagonal set Δ={$(x,x) : x∈[0,1]$} is a closed subset of $I_2$. Hence Δ$\in(I_2)=\mathcal{B}(I)×\mathcal{B}(I)⊂\mathcal{B}(I)×\mathcal{B}(I)$. Therefore, the characteristic map $1_Δ$ is measurable for the measure induced on $X×Y$. However, we have on one side $\int_{I}(\int_{I}1_Δ(x,y)dm(y))dλ(x)=\int_{I}(\int_{I}1_{x}(y)dm(y))dλ(x)=\int_{I}m({x})dλ(x)=λ(I)=1$
and on the other side
$\int_{I}(\int_{I}1_Δ(x,y)dλ(x))dm(y)=\int_{I}( \int_{I}1_{y}(x)dλ(x))dm(y)=\int_{I}λ({y})dm(y)=\int_{I}0 dm(y)=0$
These are not equal and Tonelli's Theorem failed. Is this right?
Also, in the case for uniqueness. I need to show that there is more than one measure $\mu$ on $\mathcal{L}[0,1]\times 2^{[0,1]}$ with the property that $\mu(E\times F)=\mu(E)$#$(F)$ (where # is the counting measure of F) for all $E\in \mathcal{L}([0,1])$ and $F\in 2^{[0,1]}$. How should I start with this?
$1$. Yes, your proof that Tonelli's theorem conclusion fails in this case is correct. The only minor correction is:
$2$. Now, let us show that there is more than one measure $\mu$ on $\mathcal{B}([0,1])\times 2^{[0,1]}$ with the property that $\mu(E\times F)=\lambda(E)\#(F)$ (where $\lambda$ is the Lebesgue measure and $\#$ is the counting measure) for all $E\in \mathcal{B}([0,1])$ and $F\in 2^{[0,1]}$.
Let $\mu_1$ be the the product measure $\lambda \times \#$. It is immediate that for all $E\in \mathcal{B}([0,1])$ and $F\in 2^{[0,1]}$, $$\mu_1(E\times F) = (\lambda \times \#) (E\times F)= \lambda(E)\#(F)$$
Let $\mu_2$ be a measure defined on $\mathcal{B}([0,1])\times 2^{[0,1]}$ by, for all $A \in \mathcal{B}([0,1])\times 2^{[0,1]}$,
$$\mu_2(A) = \sum_{y\in[0,1]} \lambda(([0,1]\times\{y\}) \cap A)$$
It is easy to see that $\mu_2$ is in fact a measure. Moreover, for all $E\in \mathcal{B}([0,1])$ and $F\in 2^{[0,1]}$, $$\mu_2(E\times F) = \sum_{y\in[0,1]} \lambda(([0,1]\times\{y\}) \cap (E\times F))=\sum_{y\in F}\lambda(E)=\lambda(E)\#(F)$$
Lets us prove that $\mu_1\neq \mu2$.
Consider the diagonal set $\Delta=\{(x,x) : x∈[0,1]\}$ again.
Note that, if $E\times F$ is a rectangle such that $\mu_1(E\times F)$ is finite, then $\lambda(E)=0$ or $F$ is a finite set. So $\Delta$ can not be covered by any countable collection of rectangles $E\times F$ with $\mu_1(E\times F)$ finite.
So $\mu_1(\Delta)=+\infty$ (in fact, we proved more: $\Delta$ is not even $\mu_1$-$\sigma$-finite).
On the other hand,
$$\mu_2(\Delta) = \sum_{y\in[0,1]} \lambda(([0,1]\times\{y\}) \cap \Delta)= \sum_{y\in[0,1]} \lambda(\{y\})=0$$