For ERP synced projects, when you create a line item for a commitment variation (or a commitment potential variation, if using a 2-tier variation setting) and the "Line Item" section of "New Line Item" is selected, Procore creates the following items:

Since both the commitment's bill of quantities and the variation's bill of quantities are reflected on the subcontractor payment application, this line item appears twice on the subcontractor payment application:

There currently is no functionality in Procore that can hide that £0 line item from the subcontractor payment application. When creating a subcontractor payment application, the £0 line item should be disregarded and only the variation line item should be billed against.