When a notification appears on the desktop via Ubuntu's built in system, if Minecraft is fullscreen, it disappears but can still be interacted with.
When you change the volume or a music source changes, a notification will pop up. This means I have to exit fullscreen, change the volume/song, and then enter fullscreen again if I don't want the bug to occur.
I am not sure if this is a bug with Ubuntu or Minecraft, but it doesn;t happen with anyother fullscreen applications.
I'm pretty sure it's just because of the way it looses focus, and you can alt-tab to get back into it.