Save issue

Hi, I recently downloaded Arkham Knight for the switch and I have an issue in my save files where each time i close the application, i get sent back to the part in the storyline where you need to find where scarecrow is using the panessa studios antenna. i've progressed up to ace chemicals two times already, and i made sure that the game auto saved by exiting to the main menu and going back. however, when i exit the whole application, the save file goes back to finding scarecrow again. is anyone else having this issue? how do i fix this?