A set is invariant with respect to its dynamics if $x(t_0)\in M \implies x(t)\in M$, this is not the case for the set $E$.
The set $E = \left\lbrace x\in \Omega \mid \dot{V}(x) = 0 \right\rbrace$ does not need to be an invariant set, since it does not consider the solution of $x(t)$.
I'll show this statement using the well known pendulum example.
The dynamics of a pendulum with friction are given by
$$ m\ell^2 \ddot{\theta} +d\dot{\theta} + mg\ell \sin(\theta) = 0, $$ and in state space form by
$$\dot{x} = f(x) = \begin{bmatrix} x_2\\ -\frac{g}{\ell} \sin(x_1) - \frac{d}{m\ell^2} x_2\end{bmatrix},$$
where $x_1 = \theta$, $x_2 = \dot{\theta}$.
The equilibria are $\bar{x}_1 = k\pi$, $k\in\mathbb{Z}=\left\lbrace\ldots,-1,0,1,2,\ldots\right\rbrace$ and $\bar{x}_2 = 0$.
Now, take the energy as the Lyapunov function candidate
$$V(x) =mg\ell\big(1-\cos(x_1)\big) + \frac{1}{2}m\ell^2 (x_2)^2$$
with its derivative
$$\dot{V}(x) = \frac{\partial V}{\partial x}f(x) = -d(x_2)^2 \leq 0.$$
The sets in LaSalle's invariance principle are
$$\begin{align}
\Omega &= \Omega_c := \left\lbrace x\in \mathbb{R}^2 \mid V(x) < c\right\rbrace\\
E &= \left\lbrace x\in \Omega \mid \dot{V}(x) = 0 \right\rbrace = \left\lbrace x \in \Omega \mid x_2 = 0\right\rbrace\\
M &= \left\lbrace 0 \right\rbrace,
\end{align} $$
where $M$ is the largest invariant set in $E$.
Now, consider the point $x = [1, 0]^\top \in E$, i.e. $\theta = 1$, $\dot{\theta} = 0$.
This point is in the set $E$, however it will not stay in $E$ because the gravity will cause the pendulum to move, i.e. $x_2 \neq 0$ leaving $E$.
Hence, for a point in the set $E$ it does not imply that $x(t_0) \in E \implies x(t)\in E$.
This is visualized in the figure below by the vector field (black arrows) and the different sets. The vector field in $E$ is pointing away from $E$.
The vector field and sets below are drawn for $m = 1$, $\ell = 1$, $g = 9.81$, $d = 1$ and $c = 8$.
