The issue in the original report was not caused by station modification; most recent of that was decades ago, possibly centuries, by game time. But station modification would cause it, or at least something similar, thanks to the alignment confusement effect.

I should probably note that while the station this issue arose on does provide fuel to the trains, I did not check if it had run out or not- but this train was sitting for way too long to have been waiting for fuel. Not only that, but once this train was cleared (by cancelling its job), the trains stuck behind it loaded and shipped out quickly, as expected.

Come to think of it, I have noticed that adding modules to the front of a station while a train is actively working at the station will confuse its later alignment positions- like they're only searched when it first arrives, and are specifically relative to the far end of the station from where it entered, rather than the actual station unit of which there can only be one. Adding or removing modul…

This started with the latest update, which included "network trains will no longer travel partially loaded when the supply is bottlenecked, and instead wait for their full reservation".

Well, now I've got a train waiting for its full reservation... when all cars for its current alignment are full and it needs to move to the next, but it's refusing to, so it's just going to be waiting forever…