Sandra, the manager, and several employees went along with a man on the phone and put Becky through a strip search ordeal. Why was the maintenance man, Harold, who came in later in the day, the only one who saw that what they were doing was wrong?
I am not entirely sure this is the right place to answer those questions. The movie is apparently based on a true story, about a prank caller who it is believed made a number of similar calls to fast-food restaurants over a number of years, the most significant incident of which appears to be the source material for the movie. Some of the people involved in this true life event ended up with criminal convictions from the actions they took that day. The victim and at least one of the members of staff subsequently sued the restaurant chain - making claims such as adequate staff training, and that they had not warned staff about prior incidents of hoax calls.
It is simply the fact from this incident that the Maintenance Man was the first person to refuse what the caller was demanding.
Your question is why? Its hard to be specific about the people here. Unfortunately it boils down to the fact that even when put in a stressful situation, psychologists have demonstrated in experiments that when being ordered by someone in authority a majority of people will do as they are told - to the point of believing they have caused significant pain, even harm to another. They key example is the Milgram Experiment from the early 1960's where subjects believed they were administering increasingly large electric shocks to someone else in an experiment about learning.
The result from this experiment and others performed shows that as many as 66% of people would follow orders to inflict what would be fatal voltages on others when ordered and/or reassured by someone in authority - even if simultaneously they are clearly stressed by the actions they are being asked to take. Amazingly in the Miligram Experiment even when the subject loses communication with the person they believe they are shocking, apparently unconscious, many still administered the final (fake) 450 volt shock.