When a credit controller is reviewing transactions in aged balances they can set the collection status of an invoice to “Disputed”. 

"Disputed" --> The customer has notified you that there is a problem with the transaction.

Therefore it would be useful, when processing a payment, that the payment auto allocations will exclude from the allocations the disputed transactions (until they are resolved).

This does not have to be an enforced rule but it can be controlled with a parameter (so it can be optional to the business).