Hehe. Now that you mentioned the 2nd thing. I'll ditto the been there and done that. It especially gets me when I set up auto-waypoints for ship manufacture, on a planet. (At the time, it was intended for putting exploration or attack vessels) But I forget about that idea when I produce a colony ship from that same planet. So, anyway, it gets produced, since it's waiting at the waypoint I simply click over to colonize it. Doh! Forgot to put PEOPLE in it. So I arrive to build a colony with no population. Anyway, I find out I need to send another ship over before I can start producing anything from that colony.
After a delay of turns like that, you know I am real careful about that ever since then. That's my fault. The mental problem with setting production waypoints is that they do exact what you ask.
They can't read your mind if you had a special condition you needed before it left the space yard. Especially since you specify exactly and how much is put into a cargo bay. I guess the one consolation for less chance of procedural mistakes, on my part, is that cargo holds can carry both people and objects. No screw ups involving the need to manage personell carriers from material ones.