FULL PRODUCT VERSION :
java version "1.8.9_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 26.121-b13, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
OS X El Capitan
Version 10.11.6

A DESCRIPTION OF THE PROBLEM :
If the StackPane's setOnMouseEntered / setOnMouseExited event is present and the Stage's new window overlaps, a problem will occur.
StackPane mouse events entered / exited at the same time when the mouse pointer over the StackPane extends between the Stage and the border.
This bug does not occur in Windows. (Same version 1.8.0_121)

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
1. Creating a StackPane
2. Event registration
this.setOnMouseEntered (event -> // log 1 );
this.setOnMouseExited (event -> // log 2 );
3. Stage generation
4. showAndWait ();
5. Overlay the Stage window on the StackPane.
6. Move the mouse pointer up and down the StackPane and Stage boundaries. 7. Check Log 1, Log 2.

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
When the mouse pointer is over the Stage, only log2 should be logged.
ACTUAL -
If the mouse pointer is over the StackPane and you move it up the Stage, log2 and log1 will be logged at the same time.

REPRODUCIBILITY :
This bug can be reproduced always.