I don't remember if this was warned, but I just picked up a job to deliver 6 crates. So I picked them up and placed them on the cargo lift, then the 6th was next to the lift for a quick up-down-up, but the 6th had disappeared when I came back down.
Presumably the game "forgot" about the crates that were not left out of the loading bay, but this obviously scuppered the quest.
Also, the 2 crates of Mundane crystals from the first job just didn't get picked up when I dropped them off. Presumably the conversation with the alien about the freight office overwrote the quest?