about 4 years ago - Avanya - Direct link
You probably won't get around disabling mods until you find the issue. I would start by disabling these, then test (wait for a bit so the AI recalculates things) and see how things work. Perhaps even make a new transport route or delete and redo one.

Hide Problems (might hide something that's an issue)
Improved Public Transport 2 (5.0.3)
TM:PE 11.4.0 STABLE

Metro Overhaul Mod might also play a role, but depending on how much you've used the mod in your city, you might not be able to load the city if you disable it.