Hi @acoconis,
This issue is likely due to a lack of parent ranks in your workbench upload, which can be fixed by adding in columns for the parent ranks of genus and species. You can find the proper documentation for this here.
Additionally, using the “must match” mapping preference within the Data Mapper can help prevent duplicating Taxon entries. You also might consider checking the Results tab to verify how many Taxon entries are being created before your final upload.
Further documentation on the mapping preferences and behavior settings can be found here.
I hope this helped!