In cases where there are duplicate SKUs from Shopify, try doing the following:
1. Check the merge files (if any): Review the merge files for duplicate SKUs.
2. MetaFields from Shopify: 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.