Search for command prompt
on the desktop app choice, right click and run as admin
type chkdsk /f /r and press enter (this is assuming hdd you are talking about is C drive
2 paragraphs will pop up, type [y] enter to agree to running it at start up and check the drive for problems.
re run defrag afterwards
Note if you run it on a SSD, command is chkdsk /f as the /r command repairs sectors, and SSD don't have sectors
Have you tried using an alternative Defrag program? See if this can help, it may show a different percentage - https://www.ccleaner.com/defraggler...