Stripe System Generated Payments and reconciliation on Xero

Stripes system generated payments are making our reconciliation difficult on Xero. 

We are unable to match incoming payments from stripe on the Xero dash board, because the invoice has already been marked as paid by a  'system generated payment' that has come from Stripe to Cin7 then synced to Xero.

I am having to manually undo and then delete the system generated payments, before I can then allocate the money from stripe. This is very time consuming

could there be an option to switch off the system generated payments created in cin7?