Prefab doesn't hold my script reference?

Hello there, So I have a Prefab that is randomly generated through a spawner in my level...however the "ScoreManager" script reference (an instance = null script) doesn't apply to the Prefab itself, either through the "apply button" or through the spawner in run-time...am I missing something? If I assign a script reference to the object, why would it un-assign itself?