I've made several train stations with track extensions exactly the same size as an empty station module, seeing as all wagons are the same size. The train on the picture can not load its cargo in both wagons, that's clear, and just something you gotta learn I guess.
Nonetheless, I think track extensions could be communicated to the player better in the future, and this train should at least be able to load a single wagon AND give an alert that something isn't right, seeing how the message itself exists.
Note that this is similar to an edge-case that was actually experienced in the train tutorial live-stream: A train had an exact reverse order of wagons to the station, and it seemed to be caused by trying to correctly align the first wagon to its respective module, but the next one couldn't be lined up because trains can't reverse while routing themselves. As a result the train ended its loading algorithm, and started reversing out of the station, flying past the correct module with unloaded items with its correct wagon, because now it was heading to its next stop.
Maybe you could try running the algo from both sides of the train almost as if it had the same stop in its schedule twice? Obvious issue might be caused with long trains reversing out to otherwise blocked track sections, so perhaps pre-fetching load order virtually might be the best option, then moving the train itself accordingly.
Sorry for posting a 2 in 1.
