The Problem does appear to be where the top most parent Category is. For one it is Category: Military and the other is Category World History for each instance of these duplicates. Though at there are cross category links as you walk through the child categories from the upper most to the final categories I have put forth.
So it seems like Military and War, World History and Categorization need to mull over these cross category duplicates.
Natalie, while I am against over categorization on WikiTree, there should be a category for both the North (Union Forces) and the South (Confederate Forces}. While in the same conflict, they were on opposing sides. We don't lump those who died in service in other conflicts in one blanket conflict only Category, Each major participant has their own categories for this. The Civil War should be held to the same standard.
Possibly the Category: Died in Military Service, United States of America, United States Civil War should be changed to Category: Died in Military Service, Union Forces, United States Civil War and along the same lines for the Confederate side: Category: Died in Military Service, Confederate States of America, United States Civil War to Category: Died in Military Service, Confederate Forces, United States Civil War and the other respective duplicates combined into those.
Does opening a can of worms fit this question??? LOL