I am running mrouted on NetBSD-3.1
  It has 2 NIC: fxp0 and fxp1.
  A server send multicast packets to fxp0.
  fxp1 has 2 IP address: 192.168.1.1/24, 192.168.2.1/24.
  If both clients 192.168.1.2 and 192.168.2.2 join the multicast group,
  My NetBSD router will send 2 copies for every multicast packet comed from
  fxp0.

I think that's because mrouted treats this as two logical interfaces.
While for stub networks one could probably optimize, in general this
can't be fixed since the reverse path forwarding check needs to be
done by prefix and interface.

I suspect that most people would say that having two prefixes on an
interface wna and doing multicast is to be avoided.