There have been many documented cases of astronauts not following direct orders during the Skylab and Apollo missions. Some of these have been publicly reprimanded but most have not. Most of the issues have been about relatively minor things - things which do not endanger the safety of anyone, but never the less have been disobedience.
What about the astronauts currently aboard the ISS? Do the astronauts exercise their own volition and flat out refuse to do some things, or do things they have been forbidden to do, or do the orders of the ground crew always come first? Is the fear of being reprimanded and thrown out of the space program big enough to ensure there are no deviations?
It is unlikely any sort an official answer could admit to any disobedience by the astronauts because of public image, but are there any 3rd party accounts or external sources that have revealed any problems?