clone doesn't have properties of prefab's script

Questions & Answers
1

public GameObject waterBottle; // The enemy prefab to be spawned.
public float spawnTime = 3f; // How long between each spawn.
public Transform spawnPoints; // An array of the spawn points this enemy can spawn from.

// Use this for initialization
void Start ()
{

	InvokeRepeating ("Spawn", spawnTime, spawnTime);
}

void Spawn ()
{
	
	int spawnPointIndex = Random.Range (0, spawnPoints.Length);

	GameObject waterbottleClone;
	waterbottleClone = Instantiate (waterBottle, spawnPoints[spawnPointIndex].position, spawnPoints[spawnPointIndex].rotation)as GameObject;
	Destroy (waterbottleClone, 6f);
}
2

is it becoz your are destroying it? Try:

 void Spawn ()
 {
     
     int spawnPointIndex = Random.Range (0, spawnPoints.Length);
     GameObject waterbottleClone; = Instantiate (waterBottle, spawnPoints[spawnPointIndex].position, spawnPoints[spawnPointIndex].rotation)as GameObject;
     // this destroys the object you just instantiated ... Destroy (waterbottleClone, 6f);
 }