In cases where there are duplicate SKUs from Shopify, try doing the following:
1. Duplicate skus in merge files: Check the merge files (if any): Review the merge files for duplicate SKUs.
2. MetaFields with name SKU: Shopify allows metafields to store custom values. Those metafields will need to be unique and cannot match a standard field, like SKU. There was one example where a Shopify store had a metafield named "SKU". This caused our system to create duplicate SKU records during import.
3. Third party app creating duplicate skus: Check if a plugin or app is being used on Shopify to offer membership or wholesale pricing in which the plugin or app creates duplicate skus to offer the variation pricing based on membership.