ADDITIONAL SYSTEM INFORMATION :
System Mac OS X 10.15.2 with OpenJDK 11 and JavaFX 11.0.2 and after JavaFX 11 5.0.1 and also JavaFX 16

A DESCRIPTION OF THE PROBLEM :
When a W window (JavaFX or system whatever) is in front of the JavaFX P panel that receives mouse events, the mouse transition from W to P generates a MouseEntered event which is normal. When the mouse returns from P to W the MouseExited event is generated (always normal) but immediately after the MouseEntered event is also generated, still for panel P.
And then if the mouse switches back from W to P, the MouseEntered event is not generated.
We reproduce the problem each time by going back and forth between W and P.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
Run the supplied source.
Position any window halfway in front of the Java window.
Go back and forth with the mouse over the two windows and see the succession of ENTERED and EXITED events.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
        "The mouse enters the java window"
ENTERED
        "The mouse enters the window above the java window"
EXITED
        "The mouse enters the java window"
ENTERED
        "The mouse enters the window above the java window"
EXITED
        "..."
ACTUAL -
        "The mouse enters the java window"
ENTERED
        "The mouse enters the window above the java window"
EXITED
ENTERED
        "The mouse enters the java window : no event generated"
        "The mouse enters the window above the java window"
EXITED
ENTERED
        "etc ...."

---------- BEGIN SOURCE ----------
import javafx.application.Application;
import javafx.scene.Scene;
import javafx.scene.layout.Pane;
import javafx.stage.Stage;

public class TestMouseEvent extends Application {
public static void main(String[] args) {
launch(args);
}

@Override
    public void start(Stage primaryStage) {
        Pane root = new Pane();
        Scene scene = new Scene(root);
        
        scene.setOnMouseEntered((event) -> System.out.println("ENTERED"));
        scene.setOnMouseExited((event) -> System.out.println("EXITED"));
        
        primaryStage.setScene(scene);
        primaryStage.show();
    }
}
---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
None, it seems that the source of the problem is at the library level.

FREQUENCY : always