Found a new one I've never heard of before.

I was deleting and laying down new shipping paths and when I restarted the game the cargo ships worked fine but the harbor/passenger cruise ships weren't showing up or spawning at the harbors, on that same new path.

But when I looked at the outside path connections there were no people there, but they were staging in the same spot the old paths had been. I hit the DELETE ghost nodes thing and it actaully found and deleted it.

But when I used move it with the SELECT EVERYTHING checked, it highlighted 2 little circles smaller than a node circle. Once I deleted that the new paths started working correctly. Nothing was visible until I used the extra option inside move it mod.