Instantiate why does the prefab change?

Question

C++ / C#

The problem is that for some reason, Instantiate creates a prefab (my prefab is a built map, with a lot of objects), but it is created modified, I don't understand why.
Below is a screenshot Where you can see that there are coins, for example, I collected them. After I went through the collider, you will understand from the code through which one, the implementation of the method begins, where there is Instantiate, but for some reason, it creates a map object, changed, i.e. those coins that I collected, he actually creates without them. prefabricated
Here is the code itself

public class SpaunZone : MonoBehaviour
{
    public bool spaun = false;
    public GameObject[] pref;
    public int indexNumber;
    public GameObject spaunPoint;
    // Use this for initialization
    void Start ()
    {
        spaun = false;
  }

    private void Update()
    {
        Spaun();
    }

    private void OnTriggerEnter2D(Collider2D collision)
    {
        if(collision.transform.tag == "Player")
        {
            spaun = true;
        }

    }

    private void Spaun()
    {
        if (spaun)
        {
            spaunPoint = GameObject.Find("SpaunZonePref");
            Instantiate(pref[indexNumber], spaunPoint.transform.position, Quaternion.identity);
            spaun = false;
            Destroy(pref[indexNumber], 2);
        }
        else
        {
            spaunPoint = null;
        }
    }
}

Answer 1

And please show in the inspector what you have links to in public GameObject[] pref;
maybe you have a link not to a prefab from the PROJECT, but a link to a PREFAB IN THE SCENE. then you will not be taken from, so to speak, resources, but a copy of the object that exists and changes in the scene will be created ..
UPD
I will bring it here so that people do not read all the comments.
In general, the point is that the prefab contained a link to ITSELF. and after instantiation - began to refer to itself in the SCENE.
it is necessary to separate the storage of links into prefabs, and the prefabs themselves.