This situation occurs if you - by accident - scan the QR-code twice while you are paying. In the Payconiq by Bancontact app for example, the camera feature becomes immediately active when you open the app. It's as if the payment flow launches for a second time. To prevent you from paying twice, an error message will be shown.
Please make sure you don't keep your device above the QR-code while you are paying. Try to avoid opening the payment link again.