Apple pay activates while scanning QR

The issue is not a QR code or scanner, just any NFC device which may read cards. If you are using something like a boarding pass, open the wallet first and select the card.

If your boarding pass is already in the wallet, and the wallet is open, the NFC will not trigger. Otherwise, if you just present your phone near a NFC reader, it will trigger the wallet to open to your default card (or default transit pass if enabled on the transit system). This is expected behavior