I’ve had the same exact issue happen to me 4 or 5 times now on long haul flights and it’s infuriating. Most recently just finished a 737 max 8 flight from KLAX → KJKF and upon landing it didn’t update the mission steps.
The worst part is if you’ve got the option to skip to descent while on the ground —the game doesn’t account for you spending 5 hours in flight and suddenly bugging out and needing to be rescued from said mission step. It thinks you’ve just started the flight and hit the skip to descent button and proceeds to gives you 1% of the money and XP.