Time Machine backup size seems to be too small
Time-machine does not back up your entire Harddrive. It excludes most of the OS files and backups to your internal harddrive.
It is possible, that you didn't notice, that your data got accidentially backed up to your internal drive. You can check it as follows.

To see how much space those local Time Machine backups are consuming, click the Apple icon on the menu bar, click About This Mac, and click the Storage heading. The “Backups” category here represents your local snapshots.

You can disable that through the terminal:
sudo tmutil disablelocal

Edit: It will then automatically purge the already created local backups