It is very easy to disable automatic check-in for one of the added passengers:
Open the "Trips" tab and select your flight.
Go to the "Boarding Pass" widget and click the "Auto Check-in" button.
On the page that opens, swipe to the left of the section with the name of the passenger for whom you want to disable automatic check-in and click on the orange button.
This will delete that passenger's information, and auto check-in will not be performed for that passenger.
Open the flight in the "Trips" tab.
Click the "Check-in" button in the "Boarding Pass" widget.
Long press the name of the passenger you want to delete. Press the "OK" button to confirm this action.