Just wanted to add that I am also facing this problem with OMV3 and mergerfs.
I don't use USB Drives, they are all SATA
Sometimes the mergerfs pool gets disconnected and it seems that transmission-bt writes in a directory under /media/mergerfs-id
After a reboot mergerfs mounts the pool under /media/mergerfs-id again, so that the local directory /media/mergerfs-id with its content is not visible
A few times I was able to solve the problem by removing the download in transmission gui and trashing its data, prior to reboot.
But now I am sitting infront of the problem again, only a few MB left. Already forgot how I fixed it last time, googling brought me to this thread.
And then a strange thing happened.
I commented out only the mergerfs pool from fstab
and disabled bittorrent service
rebooted
got a call from pissed off wife because she was watching a TV show, this is not the strange thing 
navigated to /media/mergerfs-id ... its empty 
checked df
2 GB free space 
I am not sure what happened, but it seems the problem solved itself.
Well, not it the long run, in the long run I would prefer that mergerfs would clear the local /media/mergerfs-id directory prior to mounting over it, that would rock, because the problem would be solved just be rebooting, not editing fstab manually.