Why is it so difficult for some people to understand that procedures are not ends in themselves but have a purpose?
Well, for a few possible reasons. People learn to be more or less decision makers or "grunts" in their working life, and different jobs require different amounts of thinking and grunting. So employees might bring legacy work behaviors into new job roles. They also learn to trust, or distrust, the outlined procedures - if, for example, they're taught that the procedures are outdated and they're expected to improvise. There's a really good chance that an employee who isn't following direction is acting on proscriptions imposed on them in previous employment or on mixed signals they're getting at work.
Also, while doing rote work comes naturally, and decision making comes naturally, too, it's hard for people to make themselves operate
simultaneously as decision makers and as cogs in the machine, which is often what people in "grunt" positions have to do, in environments where the line between these roles isn't always clear. (Take customer service roles - it's one reason why so many customer service professionals seem so stupid to the customers.) So for any given task, if their role isn't clear to them, they often weigh in too much on the decision-making side or on the just-doing-my-grunt-job side.
I have no idea of the specific work dynamic where you are, but having been both a grunt and management in my time, I've learned that most (but not all) of this kind of behavior can be prevented by understanding where it's coming from.
For example, an employee encounters a problem in the workflow. The following scenarios may explain it and need different solutions:
1) The employee doesn't identify it as a problem. It may be that he or she is being "thick," but it may also be that there's a communication and training issue here, and the trainer needs to make sure the employee understands stop signals.
2) The employee doesn't know the accepted procedure for handling the problem. That may be because the employee can't keep a thought in his head, but it might also be a training issue.
3) The employee recognizes there's a problem, knows the regular procedure, but encounters an additional problem and doesn't know what resources are available to resolve things. This is where a lot of employees try to problem solve on their own. Now, the "additional problem" may be a real issue (like something not outlined in the procedure manual), or it may not, but this kind of thing happening can usually help you identify areas where more task steps, communication, and/or training are needed.