Solution - In this specific case, customer was creating a product in Salesforce that uses a slab Discount Schedule. He was adding one Rate Plan and one tiried price charge to it. When syncing this Product to Zuora, it was creating the Rate Plan for each price book, and each rate plan had two identical charges, each with a tiered price plan.
On investigating we found that there is a field on the Product where we can link the "Discount Schedule" along with adding it to the related list as shown below.
We were able to resolve this issue by removing the Discount Schedule from the lookup field on the Product.
