CrI3 represents one of the most important van der Waals systems on the route to understanding 2D magnetic phenomena. Being arranged in a specific layered structure, it also provides a unique opportunity to investigate structural transformations in dimension-confined systems. CrI3 is dimorphic and possesses a higher symmetry low-temperature phase, which is quite uncommon. It contrasts with vanadium trihalides, which show a higher symmetry high-temperature phase. An explanation of this distinct behavior, together with a large cycle-dependent transition hysteresis, is still an open question. Our low-temperature X-ray diffraction study conducted on CrI3 single crystals complemented by magnetization and specific heat measurements was focused mainly on specific features of the structural transition during cooling. Our results manifest that the structural transition during cooling relates to the formation of structural domains despite the lower symmetry structure transforming to a higher symmetry one. We propose that these domains could control the size of thermal hysteresis.