I see this a lot in the early stages of the game (not with millions of $, of course). Trains usually run for months, and it can make a huge difference if they arrive three or four times a year. Trains are, in my experience, rarely spaced out evenly, so one train on a line might arrive just after another one at the station, so there’s not enough people to fill it, but it may be better next time. Industries seem to produce things in batches, so if a train arrives at an unfortunate time, it may not fully load. And similar things – when running a lot of lines (or, in the beginning, only a few), these effects can add up quickly.