When you make a GoCardless transaction it’ll record the payment etc for you. Then when you import bank feeds through your Current Account it’ll bring it in again.
I understand you can match the payment and it should overwrite the payment but it still brings in the transaction when it’s already been recorded, which will cause an issue.
However, when a GC transaction is made we do a transfer from GC to the current account so the current account should be in sync.
Have you contacted support about this?