I sometimes obtain NoSuchElementException exception:
It's happen when BaseGame calls InputSystem.update();
In AWTMouseInput is loop for events handling and removing from queue:
Just for reference; I've never used AWTMouseInput, I tend to use customised versions of AbsoluteMouse and ThirdPersonMouseLook.
Having now looked at the source for the AWTMouseInput, I can safely say that I'm no closer to understanding the cause One possible multithreaded scenario that could cause the problem would the one thread inside update() while another is adding to the list
Unfortunately the frequency given for the problem means very little as you've not given the context of use (such as occurs y times over xxx hours of use).
Anyway, after re-reading you're first post I realise you must be using a child the SimpleGame or SimplePassGame, which does make matters easier, as the game loop is executed in the Main thread (as that's the thread that calls start()).
Now I realise I also got the wrong end of the stick with regard to the mouse input, it'll be a runtime choice rather then compile time (so you would not have necessarily explicitly chosen it).
To me, the likely cause is a conflict caused by the Awt/Swing and Main threads.
The Awt/Swing thread puts the events in the list and the Main thread removes them, and as the LinkedList is not synchronized there would be a problem when the Main thread tried to manage the list at the same moment in time as the Awt/Swing thread tried to manage the list (assuming non atomic operations).
Btw, the runtime implementation I use, and have had no problems with in multi threaded use is com.jme.input.lwjgl.LWJGLMouseInput
…and my suggested solutions would be to use the LWJGLMouseInput instead of the AWTMouseInput
I firstly initializing LWJGL. When initialization fails I'll try JOGL, becouse on some kinds of old/easy graphics LWJGL is not functional but JOGL runs with older OpenGL, so I develop on more comupers for best performance.