Since the Application badge you can only show numbers and you are passing a longer number than it can display it will truncate the number.
It will truncate the middle part of the number, this is why it is display ..
in the middle since it can't fit the number.
Since this is all handled by iOS there is nothing you can to to change the way it is presented.
If you want you can check the badge number server side and make sure that it not exceed 9999
.