These will all be fixed in the next version.The thought just came to mind that it might be interesting to let merchant ships hurry production (like lesser Great Engineers, or Soldiers of Kilmorph) or add culture (like lesser Great Bards, or basic disciples), in which case I'd also want the Hurry and Great Works mission to also unload rather than kill their cargo. I cannot currently think of a scenario when I might want a unit with cargo to be sacrificed for a golden age or a technology, but you might as well make those missions unload cargo before killing the unit too if the code is simple enough.
I think caravels are also not allowed to enter cities in BtS (except with open borders).
Something like this is probably best, so the cargo units cannot cast spells, for example. But I'll tackle that after the next release.Maybe it would be better to exclude ships that are currently carrying cargo, or which have cargo that is not also bRivalTerritory?