Missing FBA fees

Account with rebates 

$0 FBA fees can be due to rebates.

When rebates are applied to an account, Amazon cancels out fees on the next orders until the rebate is covered.

Rebates are applied automatically to the next fulfillment fee transaction that is charged to the Seller's account. If a rebate was applied against the FBA pick and pack fee, it will appear as a reduced fee. If the rebate covered the entire fulfillment fee, the line item will not appear for the selected order payment.

Orders with deferred transaction status

A transaction is marked as deferred while an order is awaiting delivery or pending buyer payment.

In most cases, transactions remain deferred for a certain period before being paid out. 

If an order ID has a deferred transaction status, the Amazon API cannot return fulfillment data until the order ID is released.

How to check if the order is under deferred status:

In Amazon Seller Central, go to the Transaction View, select “Deferred Transactions” from the “Transaction Status” drop-down, and click Update. 

This view shows the deferral reasons and expected release dates.