Apparently the kernel function to delete the subvolume/snapshot failed: Btrfs.cc(deleteSnapshot):407 - delete snapshot failed, ioctl(BTRFS_IOC_SNAP_DESTROY) failed, errno:39 (Directory not empty) Maybe you have created a subvolume inside the subvolume. You can use "btrfs subvolume list -p /" to list all subvolume including the parent ID.