We don't yet have a reproduceable scenario in our complex JavaFX but we managed to produce the following stack more often lately.

The problem is once the application gets into this state it is broken until you restart it. I think that the loop there should do a defensive index check and just log an error.

java.lang.ArrayIndexOutOfBoundsException: -1
at java.util.ArrayList.elementData(ArrayList.java:418)
at java.util.ArrayList.get(ArrayList.java:431)
at com.sun.javafx.collections.ObservableListWrapper.get(ObservableListWrapper.java:89)
at com.sun.javafx.collections.VetoableListDecorator.get(VetoableListDecorator.java:306)
at javafx.scene.Parent.updateCachedBounds(Parent.java:1591)
at javafx.scene.Parent.recomputeBounds(Parent.java:1535)
at javafx.scene.Parent.impl_computeGeomBounds(Parent.java:1388)
at javafx.scene.layout.Region.impl_computeGeomBounds(Region.java:3078)
at javafx.scene.Node.updateGeomBounds(Node.java:3579)
at javafx.scene.Node.getGeomBounds(Node.java:3532)
at javafx.scene.Node.getLocalBounds(Node.java:3480)
at javafx.scene.Node.updateTxBounds(Node.java:3643)
at javafx.scene.Node.getTransformedBounds(Node.java:3426)
at javafx.scene.Node.updateBounds(Node.java:559)
at javafx.scene.Parent.updateBounds(Parent.java:1719)
at javafx.scene.Parent.updateBounds(Parent.java:1717)
at javafx.scene.Parent.updateBounds(Parent.java:1717)
at javafx.scene.Scene$ScenePulseListener.pulse(Scene.java:2404)
at com.sun.javafx.tk.Toolkit.lambda$runPulse$30(Toolkit.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.tk.Toolkit.runPulse(Toolkit.java:354)
at com.sun.javafx.tk.Toolkit.firePulse(Toolkit.java:381)
at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:510)
at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:490)
at com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$404(QuantumToolkit.java:319)