The df output is correct.
The storage used is by partition.
If you ever had a /home under / (on the same partition)and put files there before creating the /home mount point and mounting a new partition there, then all those files are still sitting under the / partition (sda3) - effectively hidden because the other partition mounted as /home (sda4) hides it. That data is "hidden", if it exists. I've seen this happen with backup partitions that weren't mounted for 1 backup job, so / got filled.
All of us have thought there was no way that files existed eating up storage over the yrs. Looking closer, I've always been able to find where the "lost space" was ... eventually. Usually, I start with the df -h command, then use the du -sh * as I move down the directory tree to find the files/directories hogging storage. Please trust us. You have files that are NOT on /home that are under sda3 on /.
I'm with steeldriver - use the CLI tools, not GUIs for this. GUIs tend to oversimplify things and might not show the truth. We care about truth here, not a pretty diagram.
Bookmarks