This study focuses on a musculoskeletal analysis of human lower extremity and associated muscle forces during different rehabilitative tasks and exoskeleton alignment models. By changing the size and orientation of the impairment levels that could be caused by the misalignment of the exoskeleton and biological knee joint, muscle stress variations were observed. This indicates an increase in force such as that generated by the Vastus lateralis muscle up to 4.3% due to a 5 mm lateral offset from an anatomically healthy knee joint location. In another setting, while a subject moved the shank through a circular trajectory using an exoskeleton support, muscle strain due to misalignment was reflected at the rectus femoris with a variation of 44%, the biceps femoris large head with 32% and the gastrocnemius muscles with 31–33% variation. These results suggest that misalignment should be taken into account while using exoskeletons with certain trajectories for knee rehabilitation purposes. Based on the shortcomings of conventional physiotherapeutic tasks, the outcome of this study can be helpful in prescribing an impactful yet convenient configuration toward a safe and promising rehabilitation process. Assessment of exoskeleton alignment during rehabilitation is important to ensure user safety with a better therapy efficacy.