Instanciated gameobject acts like it's a prefab.

Im working on modular space ships, customizable by the player. A ship has hardpoints, which hold modules, which in turn can hold more modules, etc. etc.

The code of a hardpoint at this moment looks very simple;

 public class Hardpoint : MonoBehaviour {
     public GameObject holds;
     public ComponentObject.Type[] canHold;
     //public int id;
     private GameObject heldInstance;
 
     public void SpawnComponent() {
         Debug.Log("SpawnComponent Called.");
         Clear();
         heldInstance = Instantiate(holds, transform.position, transform.rotation) as GameObject;
         heldInstance.transform.SetParent(transform);
     }
 
     public void RollThroughDecompression(CompressedComponent c) {
         Debug.Log("Rolling through Decompression.");
         heldInstance.GetComponent<ComponentObject>().Decompress(c);
     }
 
     public void Clear() {
         foreach (Transform child in transform)
         {
             Destroy(child.gameObject);
         }
     }
 }

however, it all acts like it's a prefab. because error messages i'm getting are: Destroying assets is not permitted to avoid data loss. If you really want to remove an asset use DestroyImmediate (theObject, true); and Setting the parent of a transform which resides in a prefab is disabled to prevent data corruption.

I'm completely lost at this point.