It's a game mechanic with a flawed design. If the inbound trains had only been spawning on one track, there never would have been a problem. If someone built a two way road and then put up a sign saying that eastbound traffic could use whichever lane they wanted up to a certain point, naturally mayhem would ensue and nobody would think that wasn't a flaw (or at least, I hope not).
I did find that having three cargo stations in my city would produce the spawning on both tracks problem, but that's not the problem itself, but rather a way to make the problem appear. If I were a CO employee writing up the bug report on this, I'd include "build three cargo train stations" in the steps to reproduce.
As a side note, to fix the problem of incoming train backlog that occurred after I deleted two of my three cargo train stations, I put back one of the stations I'd removed and added a cargo harbor near where the other one had been. It took a while, but the traffic problems from having too few train stations have mostly settled down.
Another interesting thing I noticed, which is likely a contributing factor to my original problem: when I was having the problem with spawning on both tracks, all of my train traffic (both cargo and passenger) was going to and from the same outside connection. Today, the traffic was split evenly between both of the outside rail connections. I have no idea what was going on there--I'd restarted the game several times before when analyzing the problem, so it wasn't just a temporary glitch. Whatever that's about, though, it might explain why I'd never seen the problem before in significantly larger cities with twice as many stations.