I've figured out my problem. I had mounted a CIF share to /mnt/my_cif_share/ but before mounting this folder already had 50GB of files in it. As far as I can tell mounting over it essentially 'hides' those files from du and similar tools.
To rectify, you can either unmount the share, and delete the 'hidden' files. Or to fix this without unmounting, you can remount your root folder using mount -o bind / /mnt and you will be able to delete the files from there.