I've just run into a bug where I sold my cargo to afford a hull repair. When I went to repair the hull the money was taken from my total, but the repair was never made. Additionally, the message that I could not afford the repair popped up. I was in Port Royale at the time. Hope this helps.
EDIT 11/30/2019: I've just run into a crash bug. When trying to rest in port without reaching the recovery limit of morale (given by the inn) the game freezes after a few days of rest. The only way to exit the game is to use task manager, unless you're in full screen. Then you have to restart.
Great game by the way!