I'm on the latest version, 1.0.14, that was just released.
The purple train had entered the Green station from the southeast, then left the same way (because I was distracted and forgot to flip the switch). So I stopped it after it fully left the station, and reversed it. I flipped the switch outside the Green station after the train fully entered the station.
The purple locomotive apparently kept going right through the mountain, while the traincars did reverse and left the station normally. But when they got to the Blue station, they kept going.
On the same level, I've also had trains explode when they enter opposite center stations at the same time, especially when it's not their target station.
I don't know if the two problems are related.
Other than that, I'm really enjoying the game, thanks for making it 🙂