  The van der Waals layered magnet $\alpha$-RuCl$_3$ offers tantalizing
prospects for the realization of Majorana quasiparticles. Efforts to understand
this are, however, hampered by inconsistent magnetic and thermal transport
properties likely coming from the formation of structural disorder during
crystal growth, postgrowth processing, or upon cooling through the first order
structural transition. Here, we investigate structural disorder in
$\alpha$-RuCl$_3$ using x-ray diffuse scattering and three-dimensional
difference pair distribution function (3D-$\Delta$PDF) analysis. We develop a
quantitative model that describes disorder in $\alpha$-RuCl$_3$ in terms of
rotational twinning and intermixing of the high and low-temperature structural
layer stacking. This disorder may be important to consider when investigating
the detailed magnetic and electronic properties of this widely studied
material.
