This can happen if, for example, you paid once in Kivra and once directly through your bank, or if a technical error occurred during the payment process.
Regardless of the cause, the fastest way to resolve this is to contact the sender of the invoice. As the recipient of your payments, they are the ones who can assist you with a potential refund.
If you notice that a payment has been registered twice, you can cancel it before the funds have been withdrawn. The method for canceling a payment varies depending on which bank you use.
You can find a list here of how different banks allow customers to cancel upcoming payments.