It might be a glitch with the cargo train station. I've also noticed that some buildings (especially the bus stations) freak out if you dare clicking on them with the building spawn points mod.
Yeah, the mod doesn't seem to work with Cargo stations.
I noticed something else strange last night too. A train that had done the full journey to the top of the map and then all the way down to the bottom, stopped on the main line, adjacent to the cargo station on the spur line, and promptly despawned, I had not changed anything else on the map since I'd left the game runnning just to observe the rail traffic.
There's something kooky going on for sure. I use an asset that's a flat concrete surface quite a lot, if I use it under/around the cargo station asset sometimes trains will spawn using that concrete slab as the "owner". Might delete all those and see if it changes the spawning behavior at all.
Anyway, I've also started using the ticket price mod for public transport. Since I want to build out a lot of infrastructure before I build the towns, I'm loosing a massive amount of money on public transport that just isn't getting used yet. The ticket price mod allows you to tweak the ticket prices for each form of transport. I didn't have to change much to turn an overall weekly city loss to a breakeven, but one interesting thing I did note, is that where a metro ticket or train ticket costs 200-300 cents, the taxi's charge 1000 cents per km... so, on a 9 tile map, getting from one side to the other using a taxi will raise ~ 5700 cents, ~9000+ on a 25 tile map... if a Cim uses a bus, for example, that revenue will likely only be 100-200 cents IIRC.... might make sense to build a town reliant on taxis more than trams/buses etc.
edit:
Dragged a bunch of assets, props, surfaces and PO's off the blank cargo station template and dumped them in the adjacent field...
.. sure enough, within a minute, a train spawned heading the other way...