What is wrong with the following method of calculating second moments using integration by parts $$\int_0^\infty x^2f(x)dx=[x^2F(x)]^\infty_0-2\int^\infty_0xF(x)dx=\infty-\infty$$
On the other hand taking $-P(X>x)$ as the integral of $f(x)$
$$-[x^2(1-F(x)]^\infty_0+2\int_0^\infty xP(X>x)dx=2\int_0^\infty xP(X>x)dx$$ provided the first term vanishes which we can assume it does.
Let us treat each case separately.
We should always avoid expressions such as $\ \infty-\infty, \ $ $\frac{0}{0}, \ $ or $\ 0\cdot \infty \ $ while working with limits. This is because even if starting in reasonable place, we can end in completely unjustified or meaningless one.
For example, it is not always true that for all sequences $a_{n},b_{n}$ $$\lim_{n\to \infty}(a_{n}+b_{n})=\lim_{n\to \infty}a_{n}+\lim_{n\to \infty}b_{n}.$$ Take for example $a_{n}=n+1$, $b_{n}=-n$. Then $$1=\lim_{n\to \infty}(n+1-n)\not=\lim_{n\to \infty}(n+1)-\lim_{n\to \infty}n=\infty - \infty = ?.$$
In our case note that $$\int_{0}^{\infty}x^{2}f(x)\mathrm{d}x := \lim_{n \to \infty}\int_{0}^{n}x^{2}f(x)\mathrm{d}x=\lim_{n\to \infty}\Bigg[[x^2F(x)]^n_0-2\int^n_0xF(x)\mathrm{d}x\Bigg].$$
This is actually true. Even more general fact can be proven:
Look here Expectation of nonnegative random variable when passed through nonnegative increasing differentiable function