Fail2ban and containers can be tricky, because under the hood, you'll often have container policies automatically inserting themselves above host policies in iptables. The docker documentation has a good write-up on how to solve it for their implementation
https://docs.docker.com/engine/network/packet-filtering-firewalls/
For your usecase specifically: If you're using VMs only, you could run it within any VM that is exposing traffic, but for containers you'll have to run fail2ban on the host itself. I'm not sure how LXC handles this, but I assume it's probably similar to docker.
The simplest solution would be to just put something between your hypervisor and the Internet physically (a raspberry-pi-based firewall, etc)