See the Stackoverflow question for a description, test case and work-around:
    http://stackoverflow.com/questions/20732100/javafx-why-does-stage-setresizablefalse-cause-additional-margins

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Test code:

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.layout.BorderPane;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.stage.Stage;
import javafx.scene.Group;

public class ResizableStageAutoSizingTest extends Application {

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

    @Override
    public void start(final Stage primaryStage) throws Exception {
        final Rectangle rectangle = new Rectangle(200, 100, Color.POWDERBLUE);

// if you use a Group, the content is in the top left corner with a white margins to the right and bottom.
        final Scene scene = new Scene(new Group(rectangle));

// if you use a BorderPane instead of a Group, the content is centered with a white margins on all sides.
// final BorderPane pane = new BorderPane(rectangle);
// final Scene scene = new Scene(pane);

// if the stage is not resizable, it will be correctly sized.
// primaryStage.setResizable(false);

        primaryStage.setScene(scene);

// workaround to fix issue.
// primaryStage.sizeToScene();

        primaryStage.show();
    }
}