I have two issues with MOM:
1- When placing an underground metro station and then adding tracks, the tracks connecting to the left of the station will act as if they were connected to ground-level tracks. The only workaround I've found is to place the station, add the tracks, destroy the station and add the station again at the exact same place.
2- Sometimes, my metro stations just stop working. Destroying them and placing them again helps but the next time I launch the game, the issue occurs again. With an increasingly extensive network, this can get very tedious to do. I did notice that this issue does not occur on ground-level and elevated metro stations.

I'm using stock metro stations and the MOM tracks. Latest version of the game with Sunset Harbor DLC among others. This has happened before in many previous cities and before Sunset Harbor.