I know I've brought this up on Twitter, but I thought I'd post here just to see if anyone else is experiencing this.
I estimate that 50-75% of my games have this behavior, which I've not noticed in pre-alpha12 builds.
Basically, somewhere around ~80 passengers served (in the second week of the game), a second square station will spawn basically right next to the initial square station. Frequently, this spawn also appears to "prevent" a square station from spawning on the opposite side of the river until late game (750+ passengers).
This isn't necessarily a bug, since it can be viewed as just one of the many random map possibilities. But the frequency since alpha12 arrived feels a lot like a pattern, and it is definitely an awkward pattern, if so.