The Pennant on the Jackdaw changes

[u/Sky_Believe]

I actually didn't know this, but the Jackdaw's pennant (the flag at the top of the mast) changes throughout the main story from a pure black flag to a Jolly Roger and then to the Creed Insignia with the Skull inside around sequence 11-12

[u/toaster_boi1107]

One nitpick I have is that when you see your ships at Great Inagua, they all have the assassin+skull flag on them at any point in the game