i think some games have diferent saves for diferent users. if you played the game... say, with a user called "Mario" save the game and then turn off the console and start a new user called "Luigi"... that new user Luigi might have his own save data and the previous saved data is in the first user "Mario"
try that. some games share saves between users like New Super mario bros U but there is others, like i think its the case of Super Mario 3D World and The legend of Zelda The Wind Waker HD that have one save for each of the users in the console.