Do you have user content added that's duplicating them? If not, could you give some examples so I can look for why there's a duplication?
The encounter builder draws from all .stock and .por files in the main HL folder, so you can open those and delete individual creatures to get rid of things from the list, although each update will put the current version of the official stock portfolios back (so that any bug fixes to the portfolios are included)
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