A deduplicated keyword list still has obvious repeats in it. Best Running Shoes sits four rows below best running shoes. Both survived, because to the tool they were never the same thing.
Where the inconsistency comes from
Different sources capitalise differently. Search Console reports queries as typed. Keyword tools title-case their output. A client's spreadsheet reflects whoever typed each row. Merge them and every term arrives in two or three casings.
Fixing it in one pass
Lowercase everything, then deduplicate. On a list assembled from multiple sources this routinely removes another 10 to 20% beyond what exact deduplication caught.
Search does not care, your list does
Google treats queries case-insensitively, so the casing was never meaningful data. It is purely an artefact of how each tool formats its export, and carrying it through analysis inflates every count you produce.
Try it: Convert Text to Lowercase on SeoWolf's Notepad.