pixel_player40085539 Doesn’t seem logical to have the option for trains to finish their job, but then not be able to spend the points earned from said jobs.
But that's always possible. When you send out a train where there's 6 hours of leeway to pick it up, the game can't stop you from doing that because you might not come back in 6 hours. If they did that, they couldn't let you send out any jobs at all, because for all it can predict the future, you might not come back in 30 days.
That's not the problem here. The problem is that you (and apparently plenty of other players, so it's not just you) were misled by the game's UI into not realizing you were already in the grace period. That's what they need to fix.
@alex775 (and thanks to Isaac for giving proper credit when I remembered wrong) suggested adding some kind of hard-to-miss overlay to the countdown icon, which seems like a good solution to me, or at least worth trying.