Parenting Instancing and Prefab issues

Can someone check if this is a bug?

I have instanced two (2) different prefabs with the syntax:

 GameObject instanceName = Instantiate (prefabName, position, rotation) as GameObject;

Which SHOULD (I believe) result in two GameObjects which are duplicates of (not references to) two prefabs.

Both objects have complex hierarchies (being animated meshes). E.g. A rifle and a soldier.

When I then run the line

 SetParent(childOfInstanceA.transform);

or

 transform.parent = childOfInstanceA.transform;

I get the all too familiar error: "Setting the parent of a transform which resides in a prefab is disabled to prevent data corruption".

If this is not a bug, please explain how to fix?