I've experienced this with the Mrowgrlrlr Vore units, not sure if it's all naval units. When a city expands across say a peninsula and you order a naval fleet to move to the other side of said peninsula, they attempt to take a shortcut and path across the land over the city tiles, and fail, then just sit there. You have to manually move them along the coast and around to get them to the other side.

Edit: Here's a screenshot example.

http://steamcommunity.com/sharedfiles/filedetails/?id=780841091

Once I click to give the movement order the ship jerks a little but stays where it is and the move order is canceled.