I think that the best way to prevent employees from going off on their own and making decisions that will effect the whole project, is to have a clear scope baseline. As a project manager you should have your scope statement, a clear work breakdown structure, and a work breakdown structure dictionary. Having a clear scope statement will outline what will be focused on and what is to be excluded. With a work breakdown structure and work breakdown structure dictionary you will have a clear definition of the job each member is supposed to perform and what their boundaries will be. In the case you describe it seems that there were no boundaries set in a WBS dictionary by the project manager.