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.
Other mistake: The "Indian Relic" and "Jesuit Cross" are said to improve your relationship with Indian chiefs and the monasteries, respectively. However, both the Indians and Jesuits are always friendly towards you, and their attitudes can not be changed, rendering these two items completely useless.