As you go through the steps to complete auto the check-in request (on the “Boarding Pass” widget of for upcoming flight) switch "Check in every trip" on/off before tapping the “Submit” button. 

If you already submitted the check-in, tap on Status > then go through all of the screens, and on the page with the Cancel button turn off "Check in every trip" 

and tap the "back button" at the top left-hand corner.