I am reading chapter 16 of Introduction to smooth manifolds by Lee and at the beginning of the chapter it is stated that an integral is clearly not invariant under coordinate transformations.

Why is that? It looks to me that it is the opposite I mean for instance if I change from cartesian to polar coordinates the integral should be the same, no matter what coordinates I use
The point here is that if you have an arbitrary manifold $M$ with no additional structure, and a function $f$ supported in a chart $\varphi \colon U \to \mathbb{R}^n$, then you can attempt to define the integral of $f$ as $$ \mathcal{I}(f; \varphi) = \int_{\varphi(U)} f \circ \varphi^{-1}. $$
However, this is not invariant under coordinate transforms, meaning that this "integral" depends on the chosen chart $\varphi$. For example, if $\psi \colon U \to \mathbb{R}^n$ is a compatible chart and $\tau = \psi \circ \varphi^{-1} \colon \varphi(U) \to \psi(U)$ is the transition map, then
$$\mathcal{I}(f; \psi) = \int_{\psi(U)} f \circ \psi^{-1} = \int_{\varphi(U)} f \cdot |\det J_{\tau}|, $$ where $J_{\tau}$ is the Jacobian of $\tau$. Thus, we expect generally that $\mathcal{I}(f; \varphi) \neq \mathcal{I}(f; \psi)$.