In this Wikipedia page it is said that the symmetry group of the rectangular cuboid (a box with three unequal dimensions) is a dihedral group $D_8$ (well, some people may call it $D_4$...)

However, I don't see how it is the case. If the symmetry group is $D_8$, there is a rotation element $r$ that has order $4$, i.e., $r^4=e$, but there is no such element in the symmetry group of the rectangular cuboid that has order $4$. Every element in the symmetry group of the rectangular cuboid seems to have order $2$ (except for the identity, of course) and I think it should be $\mathbb{Z}_2 \times \mathbb{Z}_2\times \mathbb{Z}_2$.
Is there anything I misunderstand here?
You are correct.
If you label the vertices $1$ through to $8$, like so . . .
. . . you get the generators:
$$\begin{align} a&=(17)(28)(35)(46),\\ b&=(13)(24)(57)(68),\\ c&=(15)(48)(26)(37),\\ x&=(14)(23)(58)(67),\\ y&=(18)(27)(36)(45),\\ z&=(12)(34)(56)(78). \end{align}$$
Putting this in GAP, we get:
This confirms your intuition.
You can confirm through direct calculation that the elements commute and each have order two. That is sufficient to conclude that it is indeed $\Bbb Z_2^3$ (as there is eight elements in total).