Steps to reproduce this issue:
1 - wait the page is completely loaded
2 - scroll horizontal scrollbar to the right (totally) or vertical scrollbar to the bottom (totally).
3 - expand the window to right
4 - move cursor on the test buttons. One or more of them will be replaced from a white rectangle. Same situation if you put buttons on the right or on the bottom of webview.

Simple code to reproduce the issue:

import javafx.application.Application;
import javafx.geometry.Pos;
import javafx.scene.Scene;
import javafx.scene.control.ProgressIndicator;
import javafx.scene.control.ToggleButton;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.HBox;
import javafx.scene.web.WebView;
import javafx.stage.Stage;

public class ScrollingIssue extends Application {

@Override
public void start(Stage stg) throws Exception {
HBox top = new HBox();
for (int i = 0; i < 3; i++) {
top.getChildren().add(new ToggleButton("TEST BUTTON " + (i + 1)));
//top.getChildren().add(new ProgressIndicator());
}
top.setAlignment(Pos.CENTER_RIGHT);
WebView view = new WebView();
BorderPane root = new BorderPane();
root.setTop(top);
root.setCenter(view);
stg.setScene(new Scene(root));
stg.show();
view.getEngine().load("http://www.oracle.com");
}
}

If you replace buttons with progress indicators you don't need to do the step 4 to reproduce this issue.