Items Counted Twice in Category/Subcategory

I have category counts turned on in my shop, but have noticed if an item is listed in both the main category and the sub-category, the item is counted twice in the main category count. I've looked but can't find anything to solve this in any of the settings.

Is there a way to fix this or am I stuck with inflated counts? I don't want to de-list the items from the main categories as I still want all the items to show on the main category's page, and not a blank listing with the list of sub-categories at the top.

I don't have any extras or tweaks on my installation; its pretty much out of the box.