First things first. I really recommend you save manually, and make a new save each time. This one is an autosave, and it's never great to have that be your main and only save. I add a number at the end each time I save, so I have CityName1, CityName2, CityName3 and so on.
I don't think this is a mod issue, I think it's the way the roads and lines are set up. You have some very long and complicated transport lines, and as far as I can tell, they're the ones that are broken. In trying to fix one, I came across this green line:
https://i.imgur.com/Jy1o2Lk.jpgNotice how it's going all over the place on the highway? It's getting trapped in all the one way roads trying to get to the next stop. It's not ideal and I get confused just looking at that image, trying to track down where it's going. :P
I would redesign the lines having problems. Try and go for some simpler shorter lines. I recommend these two video tutorials to get some ideas for how to more efficiently set up your public transport lines.
https://youtu.be/MMCD1SHNUCYhttps://youtu.be/yvusVD0Y5-c