The set of /run, /sys, /dev, and /proc are partitions that are mounted by the init process.
If the container is really stopped, then when LXD is about to restart, it should not start the container.
My understanding is that LXD tries to restart this container because it did not registered earlier that it has been stopped.
Try the following:
$ lxc config get container1 boot.autostart
true
If you get true, it means that container1 autostarts when LXD starts.
In that case, change to not autostart:
$ lxc config get container1 boot.autostart false
and then restart LXD.