The directed self-assembly of block copolymer thin films offers promise for next-generation lithography, providing access to small feature dimensions for electronic devices. Defective assembly, wherein the block copolymer does not assemble in alignment with an underlying template, is a well-known and enduring problem facing this technology. Resolving this challenge requires detailed understanding of the kinetics of defective assembly as well as the three-dimensional structure of defects. Recent experiments in this direction have revealed the existence of a unique "stitched" morphology and have examined the kinetics of its assembly and annihilation. However, a computational perspective has not yet been provided. In this work, we analyze the formation of the stitched morphology from a disordered state, provide understanding as to its genesis and stability, and explore its annihilation into aligned lamellae. We find that the topography of the guiding template in conjunction with the thickness of the film provides stability to this unique morphology. Furthermore, we find that the stitched morphology's annihilation is significantly enhanced by the presence of nearby aligned lamellae, consistent with experiments. Finally, we demonstrate that the stitched morphology is predicted to form from unbiased simulations, lending validity to experimental observations of this peculiar morphology.