Had a similar problem, when trying to upgrade DSM software, I was warned that there is not enough space on system area
du -xmd 2
showed me that I have an /volumeUSB2/ directory on the root filesystem.
I assume, when I plugged in a portable disk and used it for downloading some files with transmission, or afterwards upon doing some copying, it made a copy to root fs.
Removed the directory and the content (also from transmission) and managed to do the upgrade