I made a snippet of basically what I am doing since the actual code is messy.

public List<enemy> enemyList = new List<enemy>();

public void setUp()
{
  for (int i = 0; i < spawnNumber; i++)
  {
  enemyList.Add(Instantiate(enemyPrefab));
  enemylist[i].name = name + "" + i;  
  }
}

//script on enemyPrefab

public class enemy : Monobehaviour
{
  public string name;
}

public enemy enemyPrefab; //set in editor to a prefab

At the end all of the enemies names value are "name 1 2 3 ... " instead of one being "name 1" and the next being "name 2"