Two things... somewhat already touched on:
1. Trying to figure out why a ship did not obey the orders
I knew I gave... freaking out and firing the ship commander... then I realize I did not "Cancel" the previous Sentry order already attached to the ship/fleet (before assigning the new order)! This was frustrating as a noob.
2. Trying to build units on a space yard ship or space yard base... designed without a cargo area.
Just doesn't work.