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Is it good to have independent thinking employees?

It is good to have strong independent employees who can make their own decisions at work, however being too much independent does not necessarily mean that there will be always something good happening out of it. 
At times it may be a sign that your employees are no longer respecting your leadership.
An article in lists a few points that will help you in calling the shots and realise that your team mates are not in your control. 
You may be happy when someone congratulates on a job well done when in reality you have no idea of what they are talking about. While you be fine as long as your team achieves something, but what if something goes wrong and you were not aware of it. 
Your team is often delayed on tasks and are missing deadlines. The team members may claim that they are too busy, however you are not sure what is consuming their time. 
When your employee suggests something and you scrap it out and then they go over your head to get it approved from your boss is a clear sign that things are way out of control and this will also create a bad name for your entire department. 
When an employee makes a mistake, he may be responsible. However you will be the one who is answerable. As manager, you should have the strategy and vision in your sights at all times and communicate them downward.