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I see this problem as well on folders. I am looking at a folder right now under which there is a project which had an item due today. I checked it off on my iPhone and synced, then when I got to work synced my desktop client. The item disappeared and the dock badge also updated appropriately, but the folder which contains the project in question is showing the wrong count, but only when collapsed. When I expand the folder, the badge disappears.

I've seen a problem like this with folders on the iPad and iPhone clients too. I had a project yesterday with about 15 items, all due yesterday. I completed them all, checked them all off, then marked the project completed. The mobile clients both insisted I had a number of due and overdue items on the folder which contained the project in question. Eventually it figured it out and updated the count correctly, but I don't know if I performed a specific trigger event to fix it.