It is very easy to disable auto check-in for one of the added passengers:
Open the "Trips" tab and choose your flight
Go to the "Boarding pass" widget and tap on the "Auto check-in" button
On the page that opens, swipe to the left the section with the name of the passenger for whom you want to disable auto check-in, and click on the orange button.
This will remove the information about this passenger and the auto check-in for him will not be performed.
Open the flight in your "Trips" tab
Tap on the "Check-in" button in the "Boarding pass" widget
Use long-tap on the name of a passenger which you wanted to delete. Tap on the "OK" button to confirm this action.