C - The theory does not explain individual differences, and why some people obey and some do not. Research evidence has found that disobedience or dissent can occur for many reasons such as personality type, gender differences and situational factors. This means that obedience is a more complex process than is being explained by agency theory.
O - It does not explain motivated issues behind obedience - French and Raven (1959) identified five bases of power held by individuals in a situation that will determine the amount of obedience shown by the people in the group. These 5 types of power - legitimate, reward, referent, expert and coercive are said to motivate and influence behaviour. These factors may offer a better explanation of obedience and certainly a better explanation for Milgrams finding in his experiment.
T - The concepts of autonomy and agency are very difficult to define and measure. Agency is a state of mind that, according to Milgram, is switched to when given an order by an authority figure. This concept is an internal mental process that cannot be directly measured, only inferred from the behaviour of an agent.