If a Cybersyn destination station is too close to an Exit rift rail, then any train that is assigned to visit that destination station will attempt to path to the Exit rift rail instead of the Entry rift rail on that surface.

e.g. I had a train station that was close enough to an Exit rift rail that the 4th and final fluid wagon was still in the Exit rift rail, so when it made its temporary stop, instead of assigning the correct rift rail ID, it assigned the ID for that Exit rift rail it was still partially inside, even though the entire train had exited the rift and emptied its contents properly.

I'm just guessing. I can't see your game scene, so I'm assuming you used at least four buildings, paired up in pairs, and that you had all the Cybersyn connections enabled on both lines, right? Actually, you only need to enable one line's connection, and then use stations with the same name—just give the entrances and exits on the other surface the same name. If you've enabled all the connections, then simply use the same name for all the buildings you've linked. You know this isn't a space elevator; its path is asymmetrical, so it can't be both an entrance and an exit.

In other words, you still actually need at least four buildings because you need to establish a return route. The key difference lies in whether you have two connections or one connection open. If there are two connections, then all four buildings will have the same name. If there's only one connection, then only the exit and entrance on the other side of the surface need to use the same name. There's no way to change this; I can't alter it.

I had two separate pairs of rift connections, I was not attempting to use a single pair of rifts as a 2-way connection.
https://imgur.com/a/1dhOt0H

The rift rail on the bottom left, the one the train is partially inside in the pic, is the one I was referring to. The train station in the pic was too close to that rift rail, which meant that before I moved the rift rail, that 4th fluid wagon was still partially inside the rift rail. As long as a train is partially inside a rift rail, it will attempt to path to that rift rail instead of the intended Entry rift rail, in this case the one to the top right of the image.

I had two separate pairs of rift connections, I was not attempting to use a single pair of rifts as a 2-way connection.
https://imgur.com/a/1dhOt0H

The rift rail on the bottom left, the one the train is partially inside in the pic, is the one I was referring to. The train station in the pic was too close to that rift rail, which meant that before I moved the rift rail, that 4th fluid wagon was still partially inside the rift rail. As long as a train is partially inside a rift rail, it will attempt to path to that rift rail instead of the intended Entry rift rail, in this case the one to the top right of the image.

ok,now I understand, I will fix it.