Just looked at those functions showing in error stack, in checkSkippedTurn(), it says: SYSTEM: No score will be generated. before the thread is killed. Therefore the good news is that these errors should not affect your scores.
And oracle says An instance of ThreadDeath is thrown in the victim thread when the Thread.stop() method is invoked. and The top-level error handler does not print out a message if ThreadDeath is never caught.
therefore the error message you see in the console could simply because robocode caught that error to make some clean-ups.
actually robocode kills your thread when you are skipping 30 turns in a row (or if you have file access, this will be increased to 240).
It somehow affects your score if you performed very well in this round :P Ok, the impact should be really small, and sometimes it may happen when you are doing bad, so it should balance, but you know... still a strange behavior.