Ships' large flags on the stern are sometimes incorrect for the time period. The ones that I've noticed are US ships using a 15 star flag and French ships using the revolutionary tricolor, both appearing during the main campaign before their actual introduction. I think they only appear on captured ships (e.g. a French ship captures a British ship at the Battle of the Chesapeake and transfers crew, then the captured ex-British ship has the tricolor), but I'm not sure.
Great game btw. Looking forward to where development goes.