The test below, when left running for some time (several minutes on my machine) starts to throw exceptions:

import javafx.animation.KeyFrame;
import javafx.animation.Timeline;
import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Group;
import javafx.scene.Scene;
import javafx.stage.Stage;
import javafx.util.Duration;

public class Test extends Application {
    @Override public void start(final Stage stage) {
        stage.setScene(new Scene(new Group()));
        stage.setWidth(400);
        stage.setHeight(400);
        stage.show();

        Timeline anim = new Timeline(new KeyFrame(Duration.millis(10),
            new EventHandler<ActionEvent>() {
                public void handle(ActionEvent ev) {
                    stage.setWidth(1000 - stage.getWidth());
                }
            }));
        anim.setCycleCount(Timeline.INDEFINITE);
        anim.play();
    }

    public static void main(String[] args){
        launch(args);
    }
}

The exception is
java.lang.NullPointerException
	at com.sun.prism.impl.BaseGraphics.drawTextureVO(BaseGraphics.java:362)
	at com.sun.prism.impl.BaseGraphics.drawTexture(BaseGraphics.java:331)
	at com.sun.prism.impl.ps.BaseShaderGraphics.drawTexture(BaseShaderGraphics.java:100)
	at com.sun.prism.impl.BaseGraphics.drawTexture(BaseGraphics.java:322)
	at com.sun.prism.d3d.D3DSwapChain.present(D3DSwapChain.java:32)
	at com.sun.javafx.tk.quantum.PaintRunnable.run(PaintRunnable.java:328)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
	at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:317)
	at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:150)
	at com.sun.prism.render.RenderJob.run(RenderJob.java:29)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at com.sun.javafx.tk.quantum.QuantumRenderer$ObservedRunnable.run(QuantumRenderer.java:67)
	at java.lang.Thread.run(Thread.java:662)

I've found something suspicious in PaintRunnable.run():
311                        disposePresentable();
312                        presentable = factory.createPresentable(scene.getPlatformView());
createPresentable() creates a SwapChain and a RTTexture, but disposePresentable() disposes SwapChain only.