Hi. The problem here is that when you play with "private trains" disabled, the default (vanilla) trainstop, wagons, trains are set to the neutral force when placed. this will then allow all players to use the trains and trainstops from any player so it can be used to make one gigant train network all over the map. but if mods add new train entities then they will belong to the players force and not the neutral force.
Solution for this problem is to use "Private Trains" setting when played with other mods so all things placed by the player will belong to them.