iOS9 popover always points to top-left corner of anchor

I had the exact same problem. I just resolved it by setting sourceRect in prepareForSegue:

override func prepareForSegue(segue: UIStoryboardSegue, sender: AnyObject?) {
    switch segue.identifier {
    case "Popover Identifier"?:
        if #available(iOS 9.0, *) {
            segue.destinationViewController?.popoverPresentationController?.sourceRect = anchorView.bounds
        }
    default:
        break
    }
}