In cases where there are duplicate SKUs from Shopify, review the following possible causes:
1. Variants do not have a sku value: Every product option must have a unique sku in your Shopify store. Please see Shopify Help: Bulk editing products and variants for instructions on updating multiple skus at once.
2. Duplicate skus in merge files: Check the merge files (if any): Review the merge files for duplicate SKUs.
3. MetaField named "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.
4. 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.