While an existing transition or presentation is occurring; the navigation stack will not be updated

This warning indicates that you are trying use UINavigationController wrongly:

pushViewController:animated: called on while an existing transition or presentation is occurring; the navigation stack will not be updated

You mentioned in the comments that you are trying to pop the ViewController using

navigationController?.popViewControllerAnimated(false)

inside completion block of UIAlertController. Therefore, you are trying to unwind from the wrong view, UIAlertController is not part of the UINavigationController stack.

Try and close the UIAlertController first, then pop the current ViewController. In other words, remove the pop from the completion block and put it inside the OK block. or use unwind segue before the alert.

Another possibility, is that you have an unused or identical duplicate in storyboard. Hence, if the unwinding operation is triggered by storyboard button, select this button and check the connectivity inspector and removed unwanted connections.

For example: the red x marked was unnecessary in my case.

I solved this using DispatchQueue.main.asyncAfter call popviewcontroller after the UIAlertController's Transition complete

1) Show Alert

2) Call pop viewcontroller after delay

DispatchQueue.main.asyncAfter(deadline: .now() + 0.5) {
    self.navigationController?.popToRootViewController(animated: true)
}

This is not best way, but it works!

i am using dispatch_async and its working. i tried to navigate back but didn't worked because navigation stack will not be updated.

let destVC = self.storyboard?.instantiateViewControllerWithIdentifier("HomeViewController") as! HomeViewController
    self.presentViewController(destVC, animated: true, completion: {() -> Void in
        dispatch_async(dispatch_get_main_queue(), {() -> Void in
            self.navigationController?.popViewControllerAnimated(true)!
        })
    })