If you complete a scenario directly in the scenario menu, the game recognises you’ve completed the scenario and earned the medal for that scenario, but in journey mode the game does not recognise you’ve completed the scenario. As a result, in order to complete the journey chapters (required for a trophy) you have to do the scenario twice if you did not do it in journey mode originally.
When you select ‘Continue Journey’ in the menu for your chosen route, you’ll be presented with two options. If you select the second option, you’ll see the Chapters for the journey and can go into them individually to complete any service/scenario/training listed.