Let $W(t)$ be continuous time white noise, that is, a wide-sense stationary (WSS) zero-mean Gaussian process with autocorrelation function $R_W (\tau) = σ^2\delta(\tau)$. Calculate the auto correlation function of $X(t) = \int_0^t W(r) dr$.
Can anyone help me understand how they get these integration limits in the following step in the calculation?

By the very definition, we have
$$\delta(\tau) = \begin{cases} 0, & \tau \neq 0, \\ 1, & \tau = 0 \end{cases}.$$
Therefore,
$$\delta(r-q) = \begin{cases} 0, & r \neq q, \\ 1, & r=q \end{cases}.$$
Suppose that $s<t$, i.e. $\min\{s,t\}= s$. For any $q \in (s,t]$ and $r \in [0,s]$ we have
$$\delta(r-q)=0$$
since $r-q<0$. Consequently,
$$\int_0^s \int_s^t \mathbb{E}(W_q W_r) \, dq \, dr = 0.$$
This implies the identity you want to prove.
The argumentation for the case $t \leq s$ works analogously; I leave it to you.