Here’s my set up. LAN cable from fibre modem connected to WAN port on Asus.I don't see a specific flag for VLAN in the vnstat documentation. Not to say it can't but it would seem to need to be associated with an interface. At least that's appears to be how this version of vnstat works.
As Jack says, this would seem to be a configuration issue. The conf file should specify the primary iface. Can you describe your setup/connection?