Missing scripts in saved prefab

So I instantiate a new game object and nest a bunch of prefab objects to it. I then add a component to each of them. When I use the SaveAsPrefabAsset in PrefabUtility it saves the game object and it's children as a new asset. Great, that's exactly what I want. But the components I added are now reported as missing inside the prefab. I'm doing all of this by script. Is there something I need to do for the instantiated components to "stick" to their respective game objects before I can save?

 

It seems like the cause of the problem was that I had multiple monobehaviours in the same file. After putting them into separate files they are no longer missing inside the prefab.