So I managed to get a small spacecraft stuck in orbit around Duna. I had plenty of data stored within the capsule and didn't want to give it all up by reloading, so I decide that I shall mount a rescue attempt! And not just to save Jebediah, but to drag the entire capsule back to Kerbin with me so I can get all that sweet, sweet science. I build a ship made specifically for the purpose, stripping away all unnecessary items and adding in a cargo module so I can snatch the capsule up and transport it home. It took a number of attempts; getting the right interplanetary trajectory, making sure I arrived in a good spot, matching up orbits, slowly but surely bringing myself in close for a rendezvous with the other ship, detaching the command pod, and finally scooping it up neatly inside the cargo bay. It took quite some time, but I managed it, all this with plenty of fuel left to get it all back home. Yay! The only problem left was that Kerbin was currently out of position. Okay, so I just need to time-warp so Duna and Kerbin are in the right positions for a good shot back. That's fine. I go to the spaceport, initiate maximum warp, wait, then stop when it's all set up. Time to switch back to the ships and start the journey...except, wait, why are the symbols for each ship so far apart? To my abject horror, I discover that somehow, the captured pod had phase-shifted through the closed cargo doors during warp drive and was now about 80000km behind the rescue ship. The doors had been closed. It was inside! And now it's outside and far away! Ffffff- So at that point, after having gone through a rather heavy amount of trial and error to get to where I was, the thought of matching up docking alignments again and doing it all over just made me say "Screw it" and reload from a previous save. And it could've been so awesome too...