First off, kudos to the guys at Ironclad - a very impressive expansion to a very impressive game!
To business, I don't know if this is an Entrenchment related bug or not...
Saved Game 1

Saved Game 2

Game 1 was pretty early in the piece, I suddenly realised that the fleet I'd assembled to backstop the pirate base wasn't where they were supposed to be.
Game 2 was much later (and I was drinking, so it may be a case of user error) after I decided to complete the "Ship Swarm" achievment.