If you get the error "The same Merchant SKU was found among Unmanaged Listings. Merchant SKU must be unique for each Amazon item" during the listing of a new product, it means that you already have an active Item with the same SKU on Amazon, and it was imported into Unmanaged Listing.
If the products are identical, you can manage the Unmanaged Item via M2E Pro instead of listing a duplicate. Please complete the following steps:
1. Apply the Stop on Channel / Remove from Listing action to the duplicate product in M2E Pro Listing.
If the products are different, you can edit the SKU of the corresponding Magento Product or enable the "SKU modification" option in the Listing Settings.