They did this a few times. For example, when you're riding from house to house with Paul Revere, the same exact NPC answers the door every time. It's a not a huge thing, but it would have been nice had they at least made them look different, even if they didn't use a different voice.
That Privateer mission with the optional objective to sink 3/3 big ships by shooting their powder. It starts with you shooting down 5 little ships which are a piece of cake, before the 3 spawn. The guys on those 5 ships died quite a few times, courtesy of no mid mission checkpoint.