Sometimes games are bugged and won't properly unlock achievements. For example achievements will work fine on Windows, but be broken in the native Linux port.
The software can also re-lock achievements you've already gained, like if a family member plays on your account and unlocks some that you were planning on earning during your playthrough. Or if you just want to reset your achievement progress for some reason.
The other day I was playing around with modding a game, and inadvertently unlocked some achievements I didn't truly earn, so I re-locked them with the achievement manager. I'll wind up unlocking them in the future during normal play.
Of course you could also use it to cheat, and instantly gain 100% completion in a title.
