Docked ships disappearing after using the 'Transport' order + mission weirdness

[MoreChainguns!]

This evening, after I had killed Bottan, I figured I might as well salvage his corpse. But, my salvaging ship was a ways away. "No problem", I thought, docking the wreck to my ship and queuing up both ships' travel commands. However, once they had arrived (I was building a new ship in the meantime), the wreck was gone! Not only that, the three initial Cavalier/Commune/Family missions (Drug Deal, Weapons Delivery, Smuggling Alcohol) had spontaneously moved about 15 sectors further towards the core than they had been originally.