The project changes course. Nobody knows why. The best safeguard against stealth variations is a well-written project plan. With a well-written project plan, there is no place to hide. Any deviation from the plan, any change in course, any mid course correction, will be self-evident.
Most stealth variations occur when the parties take shortcuts.
They do not prepare a detailed project plan. Don't get me wrong. I have nothing against variations. They are perfectly okay. Do yourself a favour.