In this work, we demonstrate that WO6 octahedra in tungsten trioxide (WO3) undergo an unusually large degree of distortion and tilting to accommodate interfacial strain. This motion strongly impacts nucleation, structure, and defect formation during the epitaxial growth of WO3 on SrTiO3(001). A metastable tetragonal phase can be stabilized by heteroepitaxy and a thickness-dependent phase transition (tetragonal to monoclinic) is observed. In contrast to misfit dislocation formation, facile WO6 octahedral deformation gives rise to three types of planar defects. The thicknesses of affected regions can range from several to tens of nanometers with graded lattice parameters, allowing the strain from interfacial lattice mismatch to be relieved gradually. These atomically resolved, unique interfacial defects may significantly alter the electronic, electrochromic, and mechanical properties of WO3 epitaxial films.