I am aware that there are multiple ways of showing that the system $\,\ddot{x}=x-x^3$ is Conservative. One of which is applying Newton's law from physics $$\frac{dE(t)}{dt}=\frac{d}{dt}\left[\frac12m\dot{x}^2+V(x)\right]=0$$ where, in this case, $$-\frac{dV(x)}{dx}=x-x^3\quad\text{and}\quad m=1.$$
However, I was wondering why the following method would not work. For a consertive system the curl is $0$ (assuming the domain of definition is simply connected), in other words, $\nabla\times\boldsymbol{F}=\boldsymbol{0}.$
The given differential equation can be written as $$\begin{cases} \dot{x(t)}=y(t) \\ \dot{y(t)}=x(t)-x^3(t)\end{cases}$$ where $\boldsymbol{F}=y\hat{i}+(x-x^3)\hat{j}.$
But $\nabla\times\boldsymbol{F}=-3x^2\hat{k}\neq\boldsymbol{0}.$
What is wrong with this reasoning?

You sort of confused the notion of "conservative force field in 3D" and the notion of "conservative force field in 1D". The theorem
is only valid in $\Bbb R^3$.
But your problem is in 1D. You should not really embed your problem into 2D or 3D (well, you can, but with care).
If you intend on embedding the problem into 3D, I first point out your error. When you want to apply the above theorem, $y$ should mean the $y$-coordinate of a position. Your quantity $y(t)$ is not the $y$-coordinate of a position, but instead is the $x$-component of velocity. The correct way to embed the problem into 3D is to define two extra equations
$$\begin{cases} \ddot{x}(t)=x(t)-(x(t))^3 \\ \ddot{y}(t)=0 \\ \ddot{z}(t)=0 \end{cases}$$
So the force field is $F(x,y,z)=(x-x^3,0,0)$, which you can calculate that $\nabla\times F=\vec 0$.
As a note, there is a generalisation of the above theorem in quote to other dimensions, including for 1D, 2D, and any dimensions higher than 3D. It goes like this:
It should be an easy verification that when $n=3$, this theorem is the same as the theorem stating a force field $F$ is conservative if and only if curl of $F$ is zero.
Also, pay special attention that the domain of $F$ has to be the whole $\Bbb R^n$ but not anything else. If the domain is something else, the theorem usually does not work.
So if you ever want to do something like calculating curl to see if a force field is conservative, you should check if the dimension of your problem is 3. If it is not, use this generalised theorem instead.
(If you are ever interested in this generalised theorem, the keyword is Poincaré lemma)