Let $X$ be a random variable with mean 0 and variance $\sigma^2$.
Then $E[X^2] = E[|X|^2]$ but when we write them as $$ E[X^2] = \text{Var}[X] + E[X]^2 = \sigma, $$ and $$ E[|X|^2] = \text{Var}[|X|] + E[|X|]^2, $$ they are not equal.
What is going on here, am I mistaken in thinking $E[X^2] = E[|X|^2]$?
There's nothing paradoxical about concluding $$ \text{Var}[X] + E[X]^2 = \text{Var}[|X|] + E[|X|]^2. $$
Intuitively, $\text{Var}[|X|]$ is (potentially) smaller than $\text{Var}[X]$ because the absolute value might erase or reduce the difference between some samples.
On the other hand, the magnitude of $E[|X|]$ is (potentially) larger than the magnitude of $E[X]$, because positive and negative values of $X$ tend to cancel each other out in $E[X]$ while they pull in the same direction in the case of $E[|X|]$.
The conclusion above just says that these two opposite effects cancel each other out exactly.