Your image is an ImageView, which is a Node. No node can appear in two scenes, or twice in the same scene graph.
To fix this, create a new ImageView, using the same image displayed in the current image (Images may be reused, even though ImageViews may not).
final Popup popup = new Popup();
final ImageView popupImage = new ImageView(image.getImage());
popup.getContent().add(popupImage);
popup.setOnShown(new EventHandler<WindowEvent>(){
@Override
public void handle(WindowEvent t) {
popupImage.setFitHeight(400);
popupImage.setFitWidth(400);
}
});
popup.show(stage);