If payment txns created as a result of Batch Entry processing ends up with “Error" status. Also, "No such payment_intent…." error is logged in the Payment txn's field “Payment Response Desc”. Then it is because Batch Entry module only works in “Pre-Authorisation” mode for Stripe and Stripe SCA.
Make sure there are no custom process builder, flow or trigger logic in our Salesforce organisation that is setting Authorise Cards(AAkPay__Authorise_Transactions__c) field of Batch Entry object to false. If you need this custom logic, then add appropriate condition in order to avoid Batch Entry records that are created against Stripe/Stripe SCA's merchant facility.