Interactions between extended π-systems are often invoked as the main driving force for stacking and crystallization of 2D organic polymers. In covalent organic frameworks (COFs), the stacking strongly influences properties such as the accessibility of functional sites, pore geometry, and surface states, but the exact nature of the interlayer interactions is mostly elusive. The stacking mode is often identified as eclipsed based on observed high symmetry diffraction patterns. However, as pointed out by various studies, the energetics of eclipsed stacking are not favorable and offset stacking is preferred. This work presents lower and higher apparent symmetry modifications of the imine-linked TTI-COF prepared through high- and low-temperature reactions. Through local structure investigation by pair distribution function analysis and simulations of stacking disorder, we observe random local layer offsets in the low temperature modification. We show that while stacking disorder can be easily overlooked due to the apparent crystallographic symmetry of these materials, total scattering methods can help clarify this information and suggest that defective local structures could be much more prevalent in COFs than previously thought. ... mehrA detailed analysis of the local structure helps to improve the search for and design of highly porous tailor-made materials.