Weird Glitch When Instantiating a Game Object

I used GameObject.Instantiate to spawn a prefab that was dragged into an array in the inspector. If I had any code that referenced this GameObject in certain ways the code would break - like it had crashed, but no errors were thrown. The ways that I found that crashed it included modifying the name (.transform.name) and Debug.Logging the object. However modifying the position and rotation was OK.

I got the code to work but don't understand why.

Original Non-Working Code:

 GameObject characterObject = GameObject.Instantiate(playerPrefabs[user.AvatarModel], spawnPoints[0].transform.position, spawnPoints[0].transform.rotation) as GameObject;

 

New Working Code:

 Component characterObjectComponent = GameObject.Instantiate(playerPrefabs[user.AvatarModel], spawnPoints[0].transform.position, spawnPoints[0].transform.rotation) as Component;
 GameObject characterObject = characterObjectComponent.gameObject;

EDIT:

 public class PlayerSpawnController : MonoBehaviour
 {
     public Transform cam;
     public Transform[] playerPrefabs;
     public Transform[] spawnPoints;
     public Transform movementPivot;
     public AudioClip spawnSound;
     public float spawnSoundVolume = 0.5f;
     public int spawnRadius = 10;
     public Transform playerCharacter;
     private static System.Random random = new System.Random();
     public Transform playerShadow;
     public Transform remotePlayerMapIcon;
     public Transform localPlayerMapIcon;
     public float mapIconHeight = 500.0f;
     private JibeActivityLog jibeLog;
     public NetworkController netController;
     public GameObject spawnParticles;
     public bool usePhysicalCharacter = false;
     public float remotePlayerNametagFullyVisibleDistance = 10.0f;
     public float remotePlayerNametagFadeDistance = 30.0f;
     public bool enableIdleAnimationWakeup = false;
     public bool enableFlyingAvatars = true;
     public bool showOwnName = true;
 
     public bool useJibeAvatarControlScripts = true;
     public string[] componentsToDisableForRemotePlayers;
 
     /// <summary>
     /// Create an avatar for the local player based on the user preferences gathered from the loader scene and (if used) dressing room
     /// </summary>
     /// <param name="user">An IJibePlayer representing the user</param>
     /// <returns>A GameObject representing the player and all associated scripts, effects, and local camera</returns>
     public GameObject SpawnLocalPlayer(IJibePlayer user)
     {
         string localPlayerName = "localPlayer";
 
         GameObject localPlayer = GameObject.Find(localPlayerName);
         print("before");
         Debug.Log("localPlayer: " + localPlayer);
 
         //Check if the user has already spawned an avatar - if they have not yet spawned an avatar, this is where the avatar is set up.
         if (localPlayer == null)
         {
             Component characterObjectComponent = GameObject.Instantiate(playerPrefabs[user.AvatarModel], spawnPoints[0].transform.position, spawnPoints[0].transform.rotation) as Component;
             GameObject characterObject = characterObjectComponent.gameObject;
             print("begina");
             characterObject.name = localPlayerName;
             print("beginb");
             Debug.Log("Change name from: " + characterObject.name);
             characterObject.name = localPlayerName;
 //            Debug.Log("Change name to: " + characterObject.name);
             characterObject.transform.localScale*=.75f;
          }
         return GameObject.FindGameObjectWithTag("Player");
      }