Pause Menu Messes Up Game

In my game I have a pause menu. I also have a button that makes the pause menu pop up. The pasue menu has buttons to resume the game and quit. I have a spawner that spawns a prefab. To make the spawner work I have a transparent button the size of the entire scene. When I click this button to make the ball spawn, the entire game stops.

Spawn Ball: using System.Collections; using System.Collections.Generic; using UnityEngine;

public class BallSpawn : MonoBehaviour { public GameObject Ball;

 // Use this for initialization
 void Start () {
     
 }
 // Update is called once per frame
 public void Update () {
     
         


 }

 public void Yep () {
     Instantiate (Ball, transform.position, Quaternion.identity);
 }

}

Pause Menu: using UnityEngine.SceneManagement;

public class PauseControllerScript : MonoBehaviour {

 public string mainMenu;

 public bool isPaused;

 public GameObject pauseMenuCanvas;

 public GameObject button;



 // Use this for initialization
 void Start () {
     
 }
 
 // Update is called once per frame
 public void Update () {
     if (isPaused) {
         pauseMenuCanvas.SetActive (true);
         Time.timeScale = 0f;
     } else {
         pauseMenuCanvas.SetActive  (false);
         Time.timeScale = 1f;

     }
         

 }

 public void Resume () {
 
     isPaused = false;

 }

 public void Quit () {
     SceneManager.LoadScene ("StartScreen");
 
 }



 public void PauseMenuOpen () {
     isPaused = true;
     button.SetActive (false);
 }

}

The pause button works though ;-)