I have attempted to use the mini trains mod, but when the train appears at the subsurface, the mini cargo wagon is in front of the mini locomotive and it is stuck in the subway. If I use a vanilla locomotive with mini cargo wagons, the cargo wagons can disappear when passing through a subway.

Can you send me your savegame with only Mini trains and Subsurface mod?

I just made a test track in the editor. I no longer have it but I will set it up again.

A simple save setup.
Hmm, now I get the results of the mini train getting stuck in the subway. Maybe I had attempted to resolve the issue and that is how it made to the sub level. But either way, mini trains do not work for me.

Here it works with vanilla

Should be fixed with the next update

Good news, thanks. I look forward to it.

Was there something incorrect with my test save? I try it now with the new version and the mini-train still does not teleport to the subsurface through the subway.

Maybe I am not something not correctly. When using vanilla trains I do the following:
When on the Nauvis surface, I am able to set the schedule for the top1 station and the subway down.
The sub1 station does appear in the schedule but not reachable. I set it with a wait of 30 seconds.
The switch to auto and travel down with the train.
When at the sub1 station, I can then add the top station to complete the schedule.

This however does not work for me with mini trains, the mini train gets stuck in the subway down and does not teleport.

Could you again send me your save to test your setup?

Opened an issue on github, save attached.

Fixed for the next release

Thank you, much appreciated.