Create a new "Qt Quick application" project.

Replace "QApplication" with "QGuiApplication" in main.cpp.

Replace contents of "main.qml" with

import QtQuick 2.3
import QtQuick.Controls 1.2
import QtQuick.Dialogs 1.2

ApplicationWindow {
    visible: true
    width: 640
    height: 480
    title: qsTr("Hello World")

    MessageDialog {
        id: exitDialog
        title: "test"
        text: "Do you want to exit ?"
        standardButtons: StandardButton.Yes | StandardButton.No
        onYes: {
            Qt.quit();
        }
    }

    onClosing: {
        exitDialog.visible = true;
        close.accepted = false
    }
}

Click on the button to close the window. The MessageDialog appears and is locked/frozen.
The following message appears in the console:

• in Qt 5.3.2:

  setGeometry: Attempt to set a size (248x87) violating the constraints(248x118 - 16777215x16777215) on window QQuickWindow/''.
  

• in Qt 5.4.0 Beta:

  setGeometryDp: Attempt to set a size (248x87) violating the constraints(248x118 - 16777215x16777215) on window QQuickWindow/''.
  

It is possible to unlock the MessageDialog by increasing its size.

With QApplication, the issue is not triggered.