If there are too many trains causing traffic jams in your game, you can fix it by reorganizing your train network.
There is an excellent explanation of how Cities: Skylines spans trains through the outside connections at https://steamcommunity.com/app/255710/discussions/0/1675812484338928634/
In summary
- Create a separate train station for each outside train connection,
- Separate the intercity and local train traffic to its own train networks.