I had the same problem - I removed this mod which of course took some streets out of my cities and rebuilt with vanilla streets. No more problem.
So it seems there is an issue, I used 2x2 lane streets with bus lanes and trees in the middle.

I have same issue too. When I load my city and then upgrade or build new roads, car route AI doesn't check new roads, so everything what needs to cross that road disappear or stop forever at junction.
When I disable this mod, the problem fixed.

I've had the same issue. Bus routes begin generating from one stop to another on some roads, but, stop spawning (the line from previous stop to proposed new stop) on others. This issue is resolved when removing this mod. Hope this will be fixed soon!

I know this is an old thread, but I think I have this problem as well.
I can't create new Bus lines, and there is (mostly) no pathfinding happening on the new roads, no deliveries, garbage piling up, no cars driving, etc. One time very few cars drove on a newly placed road, but extremely slowly and they despanwned after a while.
Bus lines that would use the bugged roads can't be created either.
But for me restarting the game after building roads fixes it... until I build new roads again.