Some aspects of ships seem broken for me--I have had several different times when creating a transport that when exiting the city it pops up in the middle of town instead at of at the harbor. Now I have a useless land-locked ship!! Just something on my machine or are others having this issue too?...
This issue was reported in beta, it's not just your machine.
The only 'solution' I ever found was the old 'save-just-before-ship-completion-and-reload-if-it-occurs.
There was also a bug where if a ship is on auto-move and its movement was blocked and so unable to finish that turns move, the 'end turn' button wouldn't work and so the game couldn't proceed, so watch for that as I never saw mention it was fixed (but may have missed it...).
