FULL PRODUCT VERSION :
java version "1.8.0_72"
Java(TM) SE Runtime Environment (build 1.8.0_72-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.72-b15, mixed mode)

Bug can be reproduced with all JavaFX versions since 2.0 and is still present in the current release.

ADDITIONAL OS VERSION INFORMATION :
1.) OS X 10.11.3: 15.3.0 Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64

2.) Windows 10 x64

3.) Linux (Ubuntu x64)

EXTRA RELEVANT SYSTEM CONFIGURATION :
Bug can be reproduced with NVidia, ATI and Intel graphics cards.

A DESCRIPTION OF THE PROBLEM :
Enabling caching can cause serious rendering bugs, even in simple demo programs. Use a region, enable caching and resize the region and disable caching afterwards causes these rendering bugs. Unfortunately, the region isn't correctly rendered and dirty areas with ugly artifacts appear.

Enabling showDirtyOpts indicates that dirty-rectangles are computed correctly. But the actual rendering is broken. Disabling dirtyOpts does not solve the problem.

Example video that shows the rendering bug: https://www.dropbox.com/s/1qwnz1sargs93l1/Cache%20Bug%2001.m4v?dl=0

Sample code: https://gist.github.com/miho/ab1fff7f483c7f7409b4

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Execute sample program shown below and enable/disable caching (e.g. press toggle-cache button once per second). 

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Correct rendering.
ACTUAL -
See https://www.dropbox.com/s/1qwnz1sargs93l1/Cache%20Bug%2001.m4v?dl=0

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
// https://gist.github.com/miho/ab1fff7f483c7f7409b4

import javafx.animation.KeyFrame;
import javafx.animation.KeyValue;
import javafx.animation.Timeline;
import javafx.application.Application;
import javafx.geometry.Pos;
import javafx.scene.CacheHint;
import javafx.scene.Scene;
import javafx.scene.control.ToggleButton;
import javafx.scene.layout.Pane;
import javafx.scene.layout.Region;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;
import javafx.util.Duration;

/**
 * This JavaFX applications demonstrates strange rendering artifacts.
 *
 * Enabling a regions {@code cache} property and resizing the region causes
 * serious rendering bugs. Te reproduce the behavior just press the toggle
 * button (e.g. once a second).
 *
 * @author Michael Hoffer <info@michaelhoffer.de>
 */
public class CacheBug01 extends Application {

    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) {
        launch(args);
    }

    @Override
    public void start(Stage primaryStage) throws Exception {

        // we print the java version to be sure that we use the right jdk
        System.out.println(
                "java-version: "
                + System.getProperty("java.version")
        );

        // create and initialize region
        // this region isn't updated and causes rendering artifacts (see below)
        Region r = new Region();
        r.setCacheHint(CacheHint.SCALE);
        r.setPrefWidth(30);
        r.setPrefHeight(30);
        r.setStyle(""
                + "-fx-border-color: red;"
                + "-fx-background-color: rgba(0,0,0,0.4);"
                + "-fx-border-color: red;");

        // resize animation (prefWidth/prefHeight properties)
        Timeline l = new Timeline(
                new KeyFrame(Duration.ZERO,
                        new KeyValue(r.prefWidthProperty(), 30),
                        new KeyValue(r.prefHeightProperty(), 30)
                ),
                new KeyFrame(Duration.seconds(2),
                        new KeyValue(r.prefWidthProperty(), 400),
                        new KeyValue(r.prefHeightProperty(), 400)
                )
        );
        l.setAutoReverse(true);
        l.setCycleCount(Timeline.INDEFINITE);
        l.play();

        // region container
        Pane pane = new Pane(r);
        pane.setPrefSize(400, 400);

        // cache toggle btn
        String cacheBtnString = "Toggle Cache: r.isCache() -> ";
        ToggleButton cacheBtn = new ToggleButton(cacheBtnString + r.isCache());
        cacheBtn.setPrefWidth(300);
        r.cacheProperty().bind(cacheBtn.selectedProperty());
        r.cacheProperty().addListener((ov) -> {
            cacheBtn.setText(cacheBtnString + r.isCache());
        });

        // root box
        VBox root = new VBox(cacheBtn, pane);
        root.setAlignment(Pos.CENTER);

        // usual scene/stage setup
        Scene scene = new Scene(root, 400, 450);
        primaryStage.setResizable(false);
        primaryStage.setScene(scene);
        primaryStage.setTitle("Cache Bug 01");
        primaryStage.show();
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Since caching is necessary during animation, no simple workaround exists.