it is quite common for the APP to show all/some flights that have been in the booking but are not in the latest version of rebooking. when it comes to schedule changes and rebookings, it can quite bothersome. also the APP tend to show (BA coded) AY flights double... I had multiple schedule changes on my Christmas ticket. a 10 leg itinerary now show 24 flights.

you can see if the flight is on the ticket by checking if the segment has a ticket number.