Keyword hierarchy issue controlled vocabulary

I'm using a controlled vocabulary to organise keywords but I notice that the Keyword List seems to either move the keywords out of the hierarchycal structure or LR automatically assigns established keywords elsewhere in the Keyword List - perhaps because they've already been used in another part of the hierarchy.

For example, the word 'cow' was selected from List A and not List B but at some point, LR also selects 'cow' from List B. Now I have two keywords 'cow' in two different hierarchies.

List A

     animals

          livestock

               cow

List B

     cow

Any ideas why this may be? Are there any particular rules to adhere to in order to keep a very tight hierarchycal structure and prevent words from being picked up elsewhere in the Keyword List?

Many thanks.