We do not support out of the box monitoring for LXC containers.
With respect to the installation issue :
We add server monitors by considering UUID of the host as unique criteria. That could be the reason agents installed in all containers points to same monitor.
To resolve this Navigate to Admin --> Server Monitor --> Settings and set the option Map/Add a server based on hostname to Yes
Once the setting is applied install the server monitoring agents in the respective containers to get it identified as unique monitors.
Installing the server monitoring agents inside containers will fetch you availability , performance metrics , processes and logs monitoring.
However this is not recommended approach as we need to do manual configurations for agent service auto restart during container reboot.