Moving a prefab clone also moves all other clones in the scene

Hello there, I'm working on a 3D combat racing game (C#) and I'm stuck with the first weapon: missile.
The homing script works good (thanks go to this guy): the player picks up the weapon crate, a missile is instantiated on the top of the car and then, by pressing the fire button, the missile is launched.
The problem is that all the missiles in the scene are launched together (e.g. enemies' ones). By now I'm using standard assets for the vehicles.

WeaponCrate.cs (attached to the weapon crate, that is a simple red cube): when the player picks up the crate, a missile clone is instantiated on the top of his car only if the weapon slot is empty.

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 
 public class WeaponCrate : MonoBehaviour {
 
     // weapons
     public GameObject missile;
 
     void OnTriggerEnter(Collider other)
     {
         // (with standard assets, players and bots collide with Payer/Bot > Colliders > ColliderBottom,
         // so we need to look for parent of parent to get the Player/Bot object)
         if (
             (other.gameObject.tag == "Player" || other.gameObject.tag == "Bot") &&
             other.transform.parent.parent.GetComponent<Player>())
         {
             pickup(other.transform.parent.parent.gameObject);
         }
     }
 
     void pickup(GameObject player)
     {
         bool pickupComplete = false;
 
         // sets player.weaponSlotFull equal to true
         if (!player.GetComponent<Player>().weaponSlotFull)
         {
             player.GetComponent<Player>().weaponSlotFull = true;
             pickupComplete = true;
         }
 
         if (pickupComplete)
         {
             Vector3 weaponPosition = player.transform.position;
             // place weapon on the roof of the player
             weaponPosition.y += 2;
 
             // instantiates weapon
             GameObject missileClone =
                 Instantiate(missile, weaponPosition, player.transform.rotation) as GameObject;
 
             // disable collisions on the object before attaching it to the player
             if (missileClone.GetComponent<Collider>()) missileClone.GetComponent<Collider>().enabled = false;
             // don't allow physics to affect the object before attaching it to the player
             if (missileClone.GetComponent<Rigidbody>()) missileClone.GetComponent<Rigidbody>().isKinematic = true;
 
             // as a child of player
             missileClone.transform.parent = player.transform;
 
             // removes object from the scene
             Destroy(gameObject);
         }
     }
 }

WeaponMissile.cs (attached to the missile prefab using the Unity interface): when the fire button is pressed, the missile is launched pointing the nearest GameObject tagged "Bot".

 using System.Collections;
 using System.Collections.Generic;
 using UnityEngine;
 
 public class WeaponMissile : MonoBehaviour {
 
     public float speed = 40.0f;
     public float torque = 2.0f;
     private Rigidbody rigidBody;
     public Transform target;
 
     // Use this for initialization
     void Start () {
                 rigidBody = transform.GetComponent<Rigidbody>();
     }
     
     // Update is called once per frame
     void Update () {
         if (Input.GetButtonDown("Fire1"))
         {
             Fire();
         }
 
     }
 
     void FixedUpdate()
     {
         if (target == null || rigidBody == null) return;
 
         rigidBody.velocity = transform.forward * speed;
 
         var targetRotation = Quaternion.LookRotation(target.position - transform.position);
         rigidBody.MoveRotation(Quaternion.RotateTowards(transform.rotation, targetRotation, torque));
     }
 
     void Fire()
     {
         // enable collisions on the missile (they were disabled when attaching to the player)
         if (gameObject.GetComponent<Collider>()) gameObject.GetComponent<Collider>().enabled = true;
         // allow physics to affect the missile (they were disabled when attaching to the player)
         if (gameObject.GetComponent<Rigidbody>()) gameObject.GetComponent<Rigidbody>().isKinematic = false;
 
         float distance = Mathf.Infinity;
 
         foreach (GameObject enemy in GameObject.FindGameObjectsWithTag("Bot"))
         {
             Vector3 diff = enemy.transform.position - transform.position;
             float actualDistance = diff.sqrMagnitude;
 
             if (actualDistance < distance)
             {
                 distance = actualDistance;
                 target = enemy.transform;
 
                 // sets player.weaponSlotFull equal to false
                 // (weapon is a child of the player, so we need to look for parent to get the Player/Bot object)
                 if (gameObject.transform.parent)
                 {
                     GameObject player = gameObject.transform.parent.gameObject;
                     if (player.GetComponent<Player>() && player.GetComponent<Player>().weaponSlotFull)
                     {
                         player.GetComponent<Player>().weaponSlotFull = false;
                     }
                 }
             }
         }
     }
 }

I've already looked to the forums but all the relevant questions have been solved by removing some static variables, which I do not use at all.

Thank you