I can reproduce this NPE only on Ubuntu with animated 3D scene.
Windows or MacOS are not affected.

Steps to reproduce:
1. Run ColorCube test.
2. Move mouse cursor over rotating cube. (Check that window is focused)
3. Press Alt+F4

java.lang.NullPointerException
at javafx.scene.Scene.pick(Scene.java:1697)
at javafx.scene.Scene.access$6900(Scene.java:169)
at javafx.scene.Scene$MouseHandler.process(Scene.java:3253)
at javafx.scene.Scene$MouseHandler.access$8100(Scene.java:3084)
at javafx.scene.Scene$MouseHandler$1.run(Scene.java:3117)
at com.sun.javafx.application.PlatformImpl$4.run(PlatformImpl.java:173)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:76)
at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at com.sun.glass.ui.gtk.GtkApplication$3$1.run(GtkApplication.java:82)
at java.lang.Thread.run(Thread.java:722)