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.
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.