Java SE (Java Platform, Standard Edition)

Yes.

I have discovered the same problem in java 16 and all the way back to java 11.
If I run the following code:
package test;

import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.layout.StackPane;
import javafx.stage.Popup;
import javafx.stage.Stage;

public class TestFX extends Application {

@Override
public void start(Stage primaryStage) {
System.out.println("javafx.runtime.version: " + System.getProperties().get("javafx.runtime.version"));
Stage stage = new Stage();
Scene scene = new Scene(new StackPane());
stage.setScene(scene);
stage.show();
Popup popOver = new Popup();
for (int i = 0; i < 99999; i++) {
popOver.show(scene.getRoot(), 1, 1);
popOver.hide();
System.out.println(i);
}
}

public static void main(String[] args) {
launch(args);
}
}
It will crash with after some iterations, it can vary.
the error stacktrace:
Exception in Application start method
Exception in thread "JavaFX Application Thread" java.lang.NullPointerException
at javafx.base/com.sun.javafx.binding.ExpressionHelper.removeListener(ExpressionHelper.java:73)
at javafx.base/javafx.beans.property.ReadOnlyBooleanPropertyBase.removeListener(ReadOnlyBooleanPropertyBase.java:67)
at javafx.graphics/javafx.stage.PopupWindow.unbindOwnerFocusedProperty(PopupWindow.java:895)
at javafx.graphics/javafx.stage.PopupWindow.doVisibleChanged(PopupWindow.java:542)
at javafx.graphics/javafx.stage.PopupWindow$1.doVisibleChanged(PopupWindow.java:111)
at javafx.graphics/com.sun.javafx.stage.PopupWindowHelper.visibleChangedImpl(PopupWindowHelper.java:63)
at javafx.graphics/com.sun.javafx.stage.WindowHelper.visibleChanged(WindowHelper.java:77)
at javafx.graphics/javafx.stage.Window$12.invalidated(Window.java:1160)
at javafx.base/javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:110)
at javafx.base/javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:145)
at javafx.graphics/javafx.stage.Window.setShowing(Window.java:1187)
at javafx.graphics/javafx.stage.Window.hide(Window.java:1212)
at javafx.graphics/javafx.stage.PopupWindow.hide(PopupWindow.java:486)
at javafx.graphics/javafx.stage.PopupWindow.lambda$new$0(PopupWindow.java:147)
at javafx.base/javafx.beans.value.WeakChangeListener.changed(WeakChangeListener.java:86)
at javafx.base/com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(ExpressionHelper.java:181)
at javafx.base/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.graphics/javafx.scene.Node$TreeShowingPropertyReadOnly.invalidate(Node.java:8479)
at javafx.graphics/javafx.scene.Node.setTreeShowing(Node.java:8436)
at javafx.graphics/javafx.scene.Node.updateTreeShowing(Node.java:8427)
at javafx.graphics/javafx.scene.Node.lambda$new$2(Node.java:1010)
at javafx.base/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360)
at javafx.base/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.base/javafx.beans.property.ReadOnlyBooleanPropertyBase.fireValueChangedEvent(ReadOnlyBooleanPropertyBase.java:78)
at javafx.base/javafx.beans.property.ReadOnlyBooleanWrapper.fireValueChangedEvent(ReadOnlyBooleanWrapper.java:103)
at javafx.base/javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:111)
at javafx.base/javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:145)
at javafx.graphics/javafx.stage.Window.setShowing(Window.java:1187)
at javafx.graphics/javafx.stage.Window.hide(Window.java:1212)
at javafx.graphics/com.sun.javafx.stage.WindowPeerListener.closed(WindowPeerListener.java:105)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassWindowEventHandler.run(GlassWindowEventHandler.java:144)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassWindowEventHandler.run(GlassWindowEventHandler.java:40)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassWindowEventHandler.lambda$handleWindowEvent$4(GlassWindowEventHandler.java:176)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
at javafx.graphics/com.sun.javafx.tk.quantum.GlassWindowEventHandler.handleWindowEvent(GlassWindowEventHandler.java:174)
at javafx.graphics/com.sun.glass.ui.Window.handleWindowEvent(Window.java:1336)
at javafx.graphics/com.sun.glass.ui.Window.notifyDestroy(Window.java:1250)
at javafx.graphics/com.sun.glass.ui.win.WinWindow._close(Native Method)
at javafx.graphics/com.sun.glass.ui.Window.close(Window.java:352)
at javafx.graphics/com.sun.glass.ui.win.WinWindow.close(WinWindow.java:316)
at javafx.graphics/com.sun.glass.ui.Application.terminate(Application.java:394)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.lambda$exit$13(QuantumToolkit.java:831)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.runWithRenderLock(QuantumToolkit.java:430)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.exit(QuantumToolkit.java:827)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$tkExit$16(PlatformImpl.java:614)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:474)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:447)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:446)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
at java.base/java.lang.Thread.run(Thread.java:831)
java.lang.reflect.InvocationTargetException
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(LauncherImpl.java:464)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication(LauncherImpl.java:363)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:78)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:567)
at java.base/sun.launcher.LauncherHelper$FXHelper.main(LauncherHelper.java:1071)
Caused by: java.lang.RuntimeException: Exception in Application start method
at javafx.graphics/com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:900)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:195)
at java.base/java.lang.Thread.run(Thread.java:831)
Caused by: java.lang.RuntimeException: could not create platform window
at javafx.graphics/com.sun.glass.ui.Window.<init>(Window.java:294)
at javafx.graphics/com.sun.glass.ui.win.WinWindow.<init>(WinWindow.java:54)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.createWindow(WinApplication.java:219)
at javafx.graphics/com.sun.javafx.tk.quantum.WindowStage.initPlatformWindow(WindowStage.java:201)
at javafx.graphics/com.sun.javafx.tk.quantum.WindowStage.init(WindowStage.java:143)
at javafx.graphics/com.sun.javafx.tk.quantum.QuantumToolkit.createTKPopupStage(QuantumToolkit.java:678)
at javafx.graphics/javafx.stage.PopupWindow.doVisibleChanging(PopupWindow.java:514)
at javafx.graphics/javafx.stage.PopupWindow$1.doVisibleChanging(PopupWindow.java:107)
at javafx.graphics/com.sun.javafx.stage.PopupWindowHelper.visibleChangingImpl(PopupWindowHelper.java:57)
at javafx.graphics/com.sun.javafx.stage.WindowHelper.visibleChanging(WindowHelper.java:73)
at javafx.graphics/javafx.stage.Window$12.invalidated(Window.java:1065)
at javafx.base/javafx.beans.property.BooleanPropertyBase.markInvalid(BooleanPropertyBase.java:110)
at javafx.base/javafx.beans.property.BooleanPropertyBase.set(BooleanPropertyBase.java:145)
at javafx.graphics/javafx.stage.Window.setShowing(Window.java:1187)
at javafx.graphics/javafx.stage.Window.show(Window.java:1202)
at javafx.graphics/javafx.stage.PopupWindow.showImpl(PopupWindow.java:472)
at javafx.graphics/javafx.stage.PopupWindow.show(PopupWindow.java:417)
at test.TestFX.start(TestFX.java:35)
at javafx.graphics/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$9(LauncherImpl.java:846)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(PlatformImpl.java:474)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(PlatformImpl.java:447)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:391)
at javafx.graphics/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(PlatformImpl.java:446)
at javafx.graphics/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:96)
at javafx.graphics/com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at javafx.graphics/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
... 1 more
Exception running application test.TestFX

I see this as a critical error because our customers experiences that popups doesn't show..

We encounter this problem regularly. I am unable to create a small program to reproduce it. The error message "could not create platform window" seems to be thrown for more than one reason. The only reproducible test case is rejected by Oracle as not a bug. The issue appears to be very low level resource management in the interaction with the kernel.
In our case, we have a dual screen application (second monitor), and after about 24 hours, regularly, JavaFX fails to create popups (Dialogs or Popups), with this exception. Our only work around is to relaunch the application every 24 hours. The issue happens regardless of our interactions with the app. There are no crons/threads in our app.
If you have a reproducible small test case, please post a bug report, so we can request Oracle to investigate and fix it.