There can be many reasons, but the most common tend to be sponsor support and poor planning. Project controls usually involve being able to collect data, but if the company culture is resistant and the project sponsor doesn't help, what you collect may be limited or provide "false" readings.
The planning is also important. During planning you should be identifying the project controls and structuring the project so they are included from the beginning. Setting up tasks in a way such that they are measurable is one way planning can have an influence on project controls. Identification of controls and communicating expectations is another important element.
There are many different forms of control, and change control is an important one also, as you have identified. Be sure the rules for changes are identified and communicated up front.