Won't run when clicked during animation.

Questions & Answers
1

The char. is patrolling waypoints. At each waypoint he will stop and an animation will play. If you click on the Char. he will run to another set of waypoints. The issue is, while the Char. is stopped at the waypoint, if you click on him, he wont run. He should run at anytime he is clicked on. Navmesh and mecanim is being used.

	void OnMouseDown()
	{
		isClicked = true;
		StartCoroutine(WaitForSomeTime());
		Vector3 markerPos = markers[Random.Range(0, markers.Length)].transform.position;
		GetComponent<NavMeshAgent>().destination =  markerPos;
		posToCheck = markerPos;
		canCheckDistance = true;

	}

	void Update ()
	{
			if (isClicked) {
				Running ();
			} else {
				if (!isClicked) 
				 
					Patrolling ();
			} 	
		}


	void Running ()
	{
		nav.speed = runSpeed;
		if (canCheckDistance) {

			if (Vector3.Distance (transform.position, posToCheck) > distanceLimit - 0.5f) {
				isClicked = false;
				canCheckDistance = false;
			}
		}
	}
	
	
	void Patrolling ()
	{
		// Set an appropriate speed for the NavMeshAgent.
		nav.speed = patrolSpeed;
		
		// If near the next waypoint or there is no destination...
		if(nav.remainingDistance < nav.stoppingDistance || waitTimeSet)
		{
			
			if(!waitTimeSet)
			{
				patrolWaitTime = Random.Range(2,4);
				anim.SetBool(patrolWayPoints[wayPointIndex].name, true);
				//Debug.Log (patrolWayPoints[wayPointIndex].name);
				patrolTimer = 0;
				waitTimeSet = true;
			}
			
			// ... increment the timer.
			patrolTimer += Time.deltaTime;
			
			//Debug.Log (patrolTimer);
			// If the timer exceeds the wait time...
			if(patrolTimer >= patrolWaitTime)
			{
				anim.SetBool(patrolWayPoints[wayPointIndex].name, false);
				if(wayPointIndex != null)
					lastPoint = wayPointIndex;
				
				wayPointIndex = Random.Range(0, patrolWayPoints.Length);
				//Debug.Log ("before last = " + lastPoint + " new = " + wayPointIndex);
				if(lastPoint == wayPointIndex)
				{
					int[] tempIntArray = new int[patrolWayPoints.Length - 1];
					int cnt = 0;
					for (int i = 0; i < patrolWayPoints.Length; i++)
					{
						if(i != lastPoint)
						{
							tempIntArray[cnt] = i;
							cnt ++;
						}
						wayPointIndex = tempIntArray[Random.Range (0,tempIntArray.Length)];
					}
					//Debug.Log ("after last = " + lastPoint + " new = " + wayPointIndex);
				}
				nav.destination = patrolWayPoints[wayPointIndex].position;
				waitTimeSet = false;
			}
		}
		else
		{
			patrolTimer = 0;
		}
	}

IEnumerator WaitForSomeTime()
	{
		waitTime = Random.Range(4,31);

	yield return new WaitForSeconds(waitTime);
	isClicked = false;
}
}
2

Had a look at this as I have most/all of your code from the last question!

Anyway change your Update to this:

    void Update ()
    {
    	if (isClicked) {
    		Running ();
    	} else if (enemySight.playerInSight) {
    		if (!isClicked) 
    		Shooting ();     
    	} else if (enemySight.personalLastSighting != lastPlayerSighting.resetPosition) {
    		//if (!isClicked) 
    			Chasing ();
    	} else {
    	if (!isClicked) 				 
    		Patrolling ();
        } 	
    }

And change the OnMouseDown to this:

void OnMouseDown()
{
	isClicked = true;
	StartCoroutine(WaitForSomeTime());
	if(anim.GetBool(patrolWayPoints[wayPointIndex].name))		// added by Mmmpies start
	{
		waitTimeSet = false;
		anim.SetBool(patrolWayPoints[wayPointIndex].name, false);
		patrolTimer = 0;
	}														// added by Mmmpies ends
	Vector3 markerPos = markers[Random.Range(0, markers.Length)].transform.position;
	GetComponent<NavMeshAgent>().destination =  markerPos;
	posToCheck = markerPos;
	canCheckDistance = true;
}

Not sure what you want to happen but it appears to work for my copy of your project.