We use self-consistent field theory (SCFT) to study the directed self-assembly of laterally confined diblock copolymers. We focus on systems where the self-assembled lamellae are oriented parallel to the selective sidewalls of the channel. While well-ordered, perfect lamellae are observed in narrow channels both experimentally and numerically, undesirable defective structures also emerge. We therefore investigate the energetics of two isolated defects, dislocations and disclinations, for various segregation strengths and channel dimensions and establish conditions that favor the formation of defects. We also determine the energy barrier and the transition path between the defective and perfect state using the string method. In the case of transitions from defective to well-ordered states, we found that only a few kT of energy is necessary to overcome the kinetic barrier and suppress the defect, sharply contrasting with the large gain in free energy (many tens of kT) that is necessary for the formation of the defect from the pristine state.