I am not quiet sure what am doing wrong in the below code. In animation parameter Happy_A boolean keep turning on and off repeatedly.

Code:

using UnityEngine;
using System.Collections;
using System.Collections.Generic;
using System.Linq; 
using UnityEngine.UI;

namespace Vuforia
{

public class L_01_gameManager : MonoBehaviour 
{
    // Vuforia Tracker Reference
	private targetTracker targetObject = null;	

	public GameObject[] correctAnswers;
	Material[] CA_mats;

	public GameObject Answer_System;
	public List<GameObject> answerPrefabs; 
	public Transform[]spawnPos;
	
    //Questions 
	public List<GameObject> L_Questions; 
	public string questionLabel;

	private bool[] S_Ans = new bool[7];
	private bool[] CA_A  = new bool[9];
	private bool[] CS_A  = new bool[9];	
	private bool[] CA_D  = new bool[2];

	// Spinner
	public Transform[] wayPoints;
	public GameObject selectionSpinner;
	private Vector3 spinner_TargetScale;

    // SolutionBox
	public GameObject solutionBox;
	private Animator  solutionBox_A;
	
	// Winnie GO
	public GameObject winnie;
	private Animator winnie_A;
	private Material winne_M;
	private bool winnieHappy_T;	

	private bool[] Anim_B = new bool[5];
	private bool[] winnie_A_B = new bool[9];


    void Start()
	{
        // Vuforia Extensions
		targetObject = GameObject.Find("ImageTarget").GetComponent<targetTracker>();
		targetObject.OnTrackingFound += trackingFound;
		targetObject.OnTrackingLost  += trackingLost;		
		
		solutionBox_A = solutionBox.GetComponent<Animator>();
		winnie_A = winnie.GetComponent<Animator>();	

		winne_M = winnie.GetComponentInChildren<SkinnedMeshRenderer>().material;
		
	}
		  

	void Update()
	{
		correctAnswers_Sys();			
		answerSys();
		spinnerAnim();
		StartCoroutine(winnieAnim());
		
	}

	public void trackingFound()
	{
		StartCoroutine(fadeEffect(1.0f,1.0f));
		StartCoroutine(NumGen());

		winnie_A.SetTrigger("Taunt_A");
	}

	public void trackingLost()
	{
		

	}

	
	IEnumerator fadeEffect(float aValue, float aTime)
	{
		float alpha = winne_M.color.a;
		for(float t = 0.0f; t < 1.0f; t += Time.deltaTime/aTime)
		{
			Color newColor = new Color (1,1,1,Mathf.Lerp(alpha,aValue,t));
			winne_M.color = newColor;
			yield return null;	
		}       
	}

	IEnumerator winnieAnim()
	{		
		if(winnie_A_B[0])
		{	
			winnie_A.SetBool("Happy_A",true);
			yield return new WaitForSeconds(1.0f);			
			//winnie_A.SetBool("Happy_A",false);
			winnie_A_B[0] = false;
		}
		if(!winnie_A_B[0])
		{
			winnie_A.SetBool("Happy_A",false);
		}

		//winnie_A.SetBool("Idle_A",true);
		yield return null;


	}

	
    void answerSys()
	{
		
		if(Input.GetMouseButtonDown(0))
		{
			Ray ray = Camera.main.ScreenPointToRay(Input.mousePosition);
			RaycastHit hit;
			if (Physics.Raycast(ray, out hit))
			{
				for (int i = 0; i<L_Questions.Count; i++)
				{
					if(hit.collider.gameObject == L_Questions[0].gameObject)
					{					
						S_Ans[0] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[0].transform.position;
					}	

					if(hit.transform.tag == "Three" && S_Ans[0])
					{
						Debug.Log("ClickedRight 3!");
						CA_A[0]= true;
						S_Ans[0] = false;
					}

					if(hit.collider.gameObject == L_Questions[1].gameObject)
					{					
						S_Ans[1] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[1].transform.position;
					}

					if(hit.transform.tag == "Five" && S_Ans[1])
					{
						Debug.Log("ClickedRight 5!");
						CA_A[1]= true;
						S_Ans[1] = false;
					}

					if(hit.collider.gameObject == L_Questions[2].gameObject)
					{					
						S_Ans[2] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[2].transform.position;
					}

						if(hit.transform.tag == "Seven" && S_Ans[2])
					{
						Debug.Log("ClickedRight 7!");
						CA_A[2]= true;
						S_Ans[2] = false;
					}

					if(hit.collider.gameObject == L_Questions[3].gameObject)
					{					
						S_Ans[3] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[3].transform.position;
					}

					if(hit.transform.tag == "Nine" && S_Ans[3])
					{
						Debug.Log("ClickedRight 9!");
						CA_A[3]= true;
						S_Ans[3] = false;
					}
						
					if(hit.collider.gameObject == L_Questions[4].gameObject)
					{					
						S_Ans[4] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[4].transform.position;
					}

					if(hit.transform.tag == "Eleven" && S_Ans[4])
					{
						Debug.Log("ClickedRight 11!");
						CA_A[4]= true;
						S_Ans[4] = false;
					}
						
					if(hit.collider.gameObject == L_Questions[5].gameObject)
					{					
						S_Ans[5] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[5].transform.position;
					}

					if(hit.transform.tag == "Five" && S_Ans[5])
					{
						Debug.Log("ClickedRight 5 Again once!");
						CA_A[5]= true;
						S_Ans[5] = false;
					}

					if(hit.collider.gameObject == L_Questions[6].gameObject)
					{					
						S_Ans[6] = true;
						questionLabel = "Selected Question index is:"+ i.ToString();	
						selectionSpinner.transform.position = wayPoints[6].transform.position;
					}

					if(hit.transform.tag == "Zero" && S_Ans[6])
					{
						Debug.Log("ClickedRight 0!");
						CA_A[6]= true;
						S_Ans[6] = false;
					}

					if(hit.collider.gameObject == L_Questions[7].gameObject)
					{						
						CA_D[0]= true;
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[7].transform.position;
					}

					if(hit.transform.tag == "Five" && CA_D[0])
					{
						Debug.Log("ClickedRight 5 Again twice!");
						CA_A[7]= true;
						S_Ans[0] = false;
					}

					if(hit.collider.gameObject == L_Questions[8].gameObject)
					{
						CA_D[1] = true;						
						questionLabel = "Selected Question index is:"+ i.ToString();
						selectionSpinner.transform.position = wayPoints[8].transform.position;
					}

					if(hit.transform.tag == "Nine" && CA_D[1])
					{
						Debug.Log("ClickedRight 9 Again once!");
						CA_A[8]= true;
						CA_D[1] = false;
					}				

					
				}
			}
		}
	}

	void correctAnswers_Sys()
	{

		CA_mats = new Material[correctAnswers.Length];	
		for(int i = 0; i<correctAnswers.Length; i++)
		{
			CA_mats _= correctAnswers*.renderer.material;*_

_ correctAnswers*.renderer.material.color = new Color(0,0,0,0);*_

* if(CA_A[0]== true)
_ {
correctAnswers[0].renderer.material.color = new Color(0,1,0,1);_
winnie_A_B[0]= true;*

* }*

* if(CA_A[1]== true)
_ {
correctAnswers[1].renderer.material.color = new Color(0,1,0,1); _
winnie_A_B[0] = true;*

* } *

* if(CA_A[2]== true)
_ {
correctAnswers[2].renderer.material.color = new Color(0,1,0,1); *_

* } *

* if(CA_A[3]== true)
_ {
correctAnswers[3].renderer.material.color = new Color(0,1,0,1); *_

* }*

* if(CA_A[4]== true)
_ {
correctAnswers[4].renderer.material.color = new Color(0,1,0,1); *_

* } *

* if(CA_A[5]== true)
_ {
correctAnswers[5].renderer.material.color = new Color(0,1,0,1); *_

* } *

* if(CA_A[6]== true)
_ {
correctAnswers[6].renderer.material.color = new Color(0,1,0,1); *_

* } *

* if(CA_A[7]== true)
_ {
correctAnswers[7].renderer.material.color = new Color(0,1,0,1); *_

* }*

* if(CA_A[8]== true)
_ {
correctAnswers[8].renderer.material.color = new Color(0,1,0,1);*_

* } *
* }*
* }*

* void spinnerAnim()*
* {*
_ selectionSpinner.transform.Rotate(Vector3.upTime.deltaTime1000,Space.World);
* }*_

IEnumerator NumGen()
* {*
* yield return new WaitForSeconds(0.7f);*
* solutionBox_A.SetBool(“slideIn”,true);*

* yield return new WaitForSeconds(1.5f);*
* numRand();*
* }*

* void numRand()*
* {*
* for(int i = 0; i<spawnPos.Length; i++)*
* {*
* int answerClone= Random.Range(0,answerPrefabs.Count); *
GameObject clone = Instantiate(answerPrefabs[answerClone],spawnPos_.position,spawnPos*.rotation)as GameObject;
clone.transform.localScale = new Vector3(0.5f,0.5f,0.5f);_

clone.transform.parent = Answer_System.transform;
_ answerPrefabs.RemoveAt(answerClone);
}*_

* }*

}
}

You are calling correctAnswers_Sys() in Update so in that CA_A[0]= true is always executed and make
winnie_A_B[0]= true .

Once CA_A[0] is set to true you are not setting it to false.

This is problem in your code. If you have any doubts ask again.

Thanks.