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This error is normally encountered after a power failure (big up to ZESA).
Generally the system will run a scan on the drive automatically when rebooting and everything will be fine. Sometimes, though, as with most things, it will fail and you will see the error :

" System appears to have been shutdown incorrectly. Press CRTL D for normal startup or give root password for maintenance."

To correct this, you will need to supply the root password. You will then be given a prompt:

root@hostname#

At the prompt you must type: fsck -y /

This will run the fsck command on the primary partition, answering YES to all questions.
Once it is done, it will say that the system needs to be rebooted. You just have to type: reboot and press enter, and it should restart without any problems.