Let me explain why it can happen. Consider of the situation that there is already a notification popup with contents of "Remove display XXX", called Popup A, shown on the internal display. It is expected that after connecting an external display, both internal and external displays show notification popup with contents of "Extending screen to XXX", called Popup B. 
In fact, when an external display is connected, MessagePopupCollection for external display is created. Then AshPopupAlignmentDelegate::OnDisplayMetricsChanged is called, which will finally call MessagePopupCollection::Update to show the popup A on the external display. Then MessageCenterImpl::RemoveNotification is called. However, it fails to close the popup A on the external display because at this moment MessagePopupCollection of the external display is still in animation. Later when the popup B is created, MessagePopupCollection::AddPopup does not work. Because the popup A and popup B share the same notification id (chrome://settings/display). It is the reason why the old notification shows on the external display.