Having done the managerial thing in a few companies, I would say that a lot of employees are reluctant to question managers, even if they are encouraged to do so.

I've got several anecdotes of trying to press my team to question technical/design/administrative decisions but for the most part, they were quite. Yes, there would be one or two people who would do so (to my appreciation), but they were the exception.

To generalize, I would say that most people would rather take instruction, follow the rules and not question authority - Its easier.

As far as creating an environment to encourage constructive feedback - Possibly creating a system that provides anonymity might increase the level of feedback.

Though in my opinion, the idea of questioning issues of instinct vs. instruction have to be an intrinsic part of a companies culture. Tough to implement if not there from the beginning.

I believe it all starts with the right people. If you have the right people in your team, i.e. open minded, willing to learn and improve etc., they will naturally tend to perpetuate the right kind of environment. It gets a lot more difficult when you have to start with people who are not necessarily open to this kind of thinking. In this situation you have to first build a whole lot of trust among the team members and management before trying to slowly introduce ideas like this. Often projects finish before such a level of trust can be established.