I was able to reproduce the problem and figure out where it stems from.
I have TextureButton with a TextureRect as a child. To add an extra layer of imaging.
Run the app and start moving the mouse over the dot. Even with a Click Mask applied the TextureButton will not honor it. It will show the hover image when hovering even outside of the Click Mask.
If you hide the TextureRect inside, the Click Mask works.
The TextureRect should have no influence over it's parent's Hover signal.