mjes, it might help to understand exactly how ingredients and variations work in EYB. When you see an ingredient listed in the Ingredients field drop-down in square brackets ([ ]) behind another ingredient, it means that the square-bracketed ingredient is a variation of the first, or "master", ingredient. If you select the square-bracketed variation from the drop-down, that is what will be listed in the recipe's Ingredients field. (The technical aspects of name and spelling variations are explained and illustrated in more detail here in the Member Indexers Administration Manual, and how to apply variations in practice is covered here in the Indexing Form Instructions.)
So when you select 'beet purée [beet pulp]' from the drop-down, the recipe will show only 'beet pulp' in the ingredients list. Putting aside any possible mismatches/misassociations you may find in the Ingredients database (which as debkellie mentioned are present, and inevitable in a database as big as EYB), 'beet purée [beet pulp]' *is* the "beet pulp"-only version you're looking for and should list. (If you wanted to list 'beet purée' instead, you'd select the stand-alone 'beet purée' master ingredient.) And when you search in Recipes for "beet pulp" (with quotes, to search that exact phrase), you'll see recipe titles containing "beet pulp" listed first, followed by recipes indexed with "beet pulp" in the ingredients list.