I have noticed that on Tees Valley Line, but possibly others, when you drive the double headed Class 31 service from Tees yard back to Darlington, there is the inability to change ends to the correct cab after doing the yard work. The game thinks that you no longer wish to drive the service. Aside from this is the problem with gradients showing in reverse in certain circumstances which I am sure you are already aware.
It might not end the service but it does not register the service as having been completed in journey mode. So it is best to use a keyboard and press Ctrl +, which will change seats and not display that pop-up. Also I can't be sure it counts any previous action points when you do that. The OCD in me...had to redo a Sand Patch journey.