A few NPCs that I commonly want to run between don't have a working autopath route between them, meaning that I have to run to an alternative spot and then autopath or just manually run.

On Oquilla's Eye running from the wharf manager (Ravikel) to Si Huram for sailing daily quest doesn't work as you get caught on the edge of the staircase.

On Illiya Island going from Maonil to the wharf manager (Dario) sometimes works but isn't fully reliable.

I am sure there are lots but these are two I am familiar with.