Simple code to reproduce the issue:

import java.util.Random;
import javafx.animation.PauseTransition;
import javafx.application.Application;
import javafx.beans.property.IntegerProperty;
import javafx.beans.property.SimpleIntegerProperty;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.scene.Scene;
import javafx.scene.control.Label;
import javafx.scene.control.TableColumn;
import javafx.scene.control.TableView;
import javafx.scene.control.cell.PropertyValueFactory;
import javafx.scene.layout.ColumnConstraints;
import javafx.scene.layout.GridPane;
import javafx.stage.Stage;
import javafx.util.Duration;

/**
 *
 * @author Alessio
 */
public class TableViewScrollIssue extends Application {

    public class TableViewItem {

        private final IntegerProperty id;
        private final IntegerProperty value;

        public TableViewItem(int id, int value) {
            this.id = new SimpleIntegerProperty(id);
            this.value = new SimpleIntegerProperty(value);
        }

        public int getId() {
            return id.get();
        }

        public IntegerProperty idProperty() {
            return id;
        }

        public int getValue() {
            return value.get();
        }

        public IntegerProperty valueProperty() {
            return value;
        }

    }

    private GridPane root;
    private TableView<TableViewItem> primaryTable;
    private TableView<TableViewItem> secondaryTable;

    @Override
    public void start(Stage primaryStage) {
        ObservableList<TableViewItem> items = FXCollections.observableArrayList();
        for (int i = 0; i < 50; i++) {
            items.add(new TableViewItem(i, (new Random().nextInt(4000))));
        }
        primaryTable = createTableView();
        primaryTable.setItems(items);
        primaryTable.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TableViewItem>() {

            @Override
            public void changed(ObservableValue<? extends TableViewItem> observable, TableViewItem oldValue, TableViewItem newValue) {
                secondaryTable.setItems(null);
                if (newValue != null) {
                    PauseTransition transition = new PauseTransition(Duration.millis(20));
                    transition.setOnFinished(new EventHandler<ActionEvent>() {

                        @Override
                        public void handle(ActionEvent event) {
                            ObservableList<TableViewItem> items = FXCollections.observableArrayList();
                            for (int i = 0; i < 100; i++) {
                                items.add(new TableViewItem(i, (new Random().nextInt(4000))));
                            }
                            secondaryTable.setItems(items);
                        }
                    });
                    transition.play();
                }
            }
        });
        secondaryTable = createTableView();
        root = new GridPane();
        ColumnConstraints col = new ColumnConstraints();
        col.setFillWidth(true);
        col.setPercentWidth(50.0);
        root.getColumnConstraints().addAll(col, col);
        root.addColumn(0, primaryTable);
        root.addColumn(1, secondaryTable);
        Scene scene = new Scene(root, 600, 400);
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    private TableView createTableView() {
        TableView<TableViewItem> view = new TableView<>();
        TableColumn<TableViewItem, Integer> colId = new TableColumn("ID");
        colId.setCellValueFactory(new PropertyValueFactory<>("id"));
        TableColumn<TableViewItem, Integer> colVal = new TableColumn("VALUE");
        colVal.setCellValueFactory(new PropertyValueFactory<>("value"));
        view.getColumns().add(colId);
        view.getColumns().add(colVal);
        view.setColumnResizePolicy(TableView.CONSTRAINED_RESIZE_POLICY);
        view.setPlaceholder(new Label());
        return view;
    }

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

Step to reproduce this issue:
- select an item in the left table
- scroll the items in the right table
- select a new item in the left table. A null pointer exception is thrown.

The pause transition is used to simulate a server request. Without that there isn't this issue.
This issues started from javafx 8u40-ea.