Continuity mistake: When you are romancing a governor's daughter, and the city she lives in is captured by another nation, a new governor with his daughter is installed. This new girl looks completely different from your old romance (and her father is a completely different person), but she nonetheless remembers you. You are still at the same stage in your relationship, even if the girl has never met you before. You can even (for instance) rescue a blonde Dutch woman from her captors, and end up returning with a black-haired Spanish girl.
Other mistake: When fighting Baron or Colonel Mendoza in ship-to-ship combat, they occasionally surrender, if you damage their ship enough. Nonetheless, you still have to fight the duel on deck with them, and your men are fighting it out off-screen despite the Spaniards having surrendered just seconds earlier.