A lot of IFs here, but:
If you have two containers, say, CT1 with eth0 and eth1, and CT2 with eth0 and eth1, and eth0 nics are in the network0, and eth1 nics are in network1, then when you run scan from CT1 to CT2 in network0, by default it will use eth0 and so on.
Can you run the following...