So... Earlier on I decided to orbit Minmus for the first time in over a year. I got there, orbited and maybe cut it a little too fine trying to get home again - I ran out of fuel with a periapsis of something like 100km, but an apoapsis of, well, quite far beyond Minmus. That orbit kept intercepting both Mun and Minmus so I got thrown about quite a lot but I figured I'd just let it keep simulating to see where I ended up.
In the end, I was left orbiting Kerbin with a periapsis of 250km and an apoapsis of 9Mm so I figured I'd try a rescue attempt. The ship I sent up was identical to the one that went to Minmus except all the science gear was replaced with an empty lander capsule. That, somehow, didn't have enough fuel to get into a rendezvous orbit, so I scrapped it, put a docking connector on, sent it up to a circular 200km orbit, sent another two copies of it up to top up the fuel tank - so far, so good.
Then I figured I had enough fuel for the rescue attempt, so I got started. I used Mechjeb (because at this point I was beyond caring about learning and just wanted it done) to plot the inclination adjustment, but just as it was about to complete the navball target started just rotating around the navball, my rocket was therefore just spinning around on an infinite loop. So I thought ok, fine, I'm 0.1 degree off so it's probably ok. Next step, the same thing happened - at the end of the burn, the target just went way off course and I had no idea where I was going, I ended up something like 200km away at the closest point. From there it pretty much just kept getting worse because the navball was basically broken, as far as I can tell, so I ended up in an almost identical orbit except shifted across and down by about 10km, and completely out of fuel.
I have no idea what I was doing wrong, in fact I'm pretty sure it wasn't me but I have no idea, maybe it was. I'm tempted to try again, this time assembling a huge ship in orbit that can't possibly run out of fuel... Or I could just abort both flights and try going to Minmus again with a slightly revised design.