Some clarifications first: Both LXC and LXD are tools to manage Linux containers. LXC is low level, LXD is a newer, more polished containers manager.
So, lxc config is LXD's way to configure a Linux container, while lxc.mount.entry = inside container's config file is LXC's lower level way to achieve the same thing.
Apparently you use LXD, so stick with it, ...
These mounts are used by running containers. In your info it appears you have 14 running containers. A prune command will not stop and delete running containers, so that isn't expected to cleanup these mounts. To remove the mount you need to stop and delete the container. Use:
docker container ls # list ...