1. Click "create control";
2. Click "set disabled";
The selected buuton ("1" by default) should be rendered over the right arrow.
If bug doesn't appear set control enabled and disabled again or
repeat steps 1, 2;

package javafxapplication68;

import javafx.application.Application;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.Pagination;
import javafx.scene.control.TextField;
import javafx.scene.layout.HBox;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class JavaFXApplication68 extends Application {

    VBox vbControlContainer;
    Pagination testedControl;
    
    @Override
    public void start(Stage stage) {

        VBox vbLeft = new VBox(20d);
        
        vbControlContainer = new VBox(5d);
        vbControlContainer.setAlignment(Pos.CENTER);
        vbControlContainer.setMinWidth(300);
        vbControlContainer.setPrefWidth(300);
        vbControlContainer.setMaxWidth(300);
        vbControlContainer.setMinHeight(300);
        vbControlContainer.setPrefHeight(300);
        vbControlContainer.setMaxHeight(300);
        vbControlContainer.setStyle("-fx-border-color:RED");
        
        VBox vbSecond = new VBox(5d);
        vbSecond.setStyle("-fx-border-color:GREEN");
        
        Button btnSetDisabled = new Button("set disabled");
        btnSetDisabled.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent t) {
                if (testedControl != null) {
                    testedControl.setDisable(true);
                }
            }
        });
        
        Button btnSetEnabled = new Button("set disabled");
        btnSetEnabled.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent t) {
                if (testedControl != null) {
                    testedControl.setDisable(false);
                }
            }
        });
        
        Button btnCreateControl = new Button("crete control");
        btnCreateControl.setOnAction(new EventHandler<ActionEvent>() {
            @Override
            public void handle(ActionEvent t) {
                testedControl = new Pagination();
                testedControl.maxPageIndicatorCountProperty().set(3);
                vbControlContainer.getChildren().clear();
                vbControlContainer.getChildren().add(testedControl);
            }
        } );
        
        vbSecond.getChildren().addAll(btnCreateControl, btnSetDisabled, btnSetEnabled);
        
        vbLeft.getChildren().addAll(vbControlContainer, vbSecond);
        
        HBox root = new HBox(20d);
        VBox vbRight = new VBox(5d);
        vbRight.setStyle("-fx-border-color:BLUE");
        
        VBox vb = new VBox(5d);
        for (int i = 0; i < 5; i++) {
            HBox hb = new HBox(5d);
            for (int j = 0; j < 10; j++) {
                hb.getChildren().add(new TextField("Label " + j));
            }
            vb.getChildren().add(hb);
        }
        
        vbRight.getChildren().addAll(vb);
        root.getChildren().addAll(vbLeft, vbRight);
        
        Scene scene = new Scene(root, 800, 600);

        stage.setScene(scene);
        stage.setTitle(System.getProperty("java.runtime.version") + "; " + System.getProperty("javafx.runtime.version"));
        stage.show();
    }

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

}