This happens when a Window is opened while a tooltip is open. The code to reproduce is unfortunately not possible to derive since it is deep into custom code that is not public.
However, the exception should be pretty self explanatory and a defensive null check should be very safe.

When the exception happens the UI locks completely and the app will have to be shut down with killall.

Uncought exception in thread Thread[JavaFX Application Thread,5,main] (Cannot invoke "com.sun.glass.ui.Window.isTransparentWindow()" because the return value of "com.sun.javafx.tk.quantum.WindowStage.getPlatformWindow()" is null)
java.lang.NullPointerException: Cannot invoke "com.sun.glass.ui.Window.isTransparentWindow()" because the return value of "com.sun.javafx.tk.quantum.WindowStage.getPlatformWindow()" is null
at com.sun.javafx.tk.quantum.GlassScene.getClearColor(GlassScene.java:334)
at com.sun.javafx.tk.quantum.SceneState.update(SceneState.java:100)
at com.sun.javafx.tk.quantum.GlassScene.updateSceneState(GlassScene.java:277)
at com.sun.javafx.tk.quantum.GlassScene.releaseSynchronization(GlassScene.java:138)
at javafx.scene.Scene$ScenePulseListener.pulse(Scene.java:2511)
at com.sun.javafx.tk.Toolkit.lambda$runPulse$2(Toolkit.java:413)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at com.sun.javafx.tk.Toolkit.runPulse(Toolkit.java:412)
at com.sun.javafx.tk.Toolkit.firePulse(Toolkit.java:439)
at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:563)
at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:543)
at com.sun.javafx.tk.quantum.QuantumToolkit.pulseFromQueue(QuantumToolkit.java:536)
at com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$11(QuantumToolkit.java:342)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
at com.sun.glass.ui.gtk.GtkApplication.enterNestedEventLoopImpl(Native Method)
at com.sun.glass.ui.gtk.GtkApplication._enterNestedEventLoop(GtkApplication.java:347)
at com.sun.glass.ui.Application.enterNestedEventLoop(Application.java:512)
at com.sun.glass.ui.EventLoop.enter(EventLoop.java:107)
at com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(QuantumToolkit.java:635)
at javafx.stage.Stage.showAndWait(Stage.java:465)