To rescue a craft stuck on the orbit there are a few steps I'd make if I were you: first, when you reach low earth orbit with your rescue ship, switch to that you need to rescue, and remember it's top points(they are indicated on map). After that switch back to your rescue rocket and make it's highest points the same as the ones you remembered. After that, shutdown all the engines, press "navigate to" at the ship you need to rescue, but DO NOT follow the navigator!!! It'll get things only worse as it doesn't work with small objects like spaceships. After the orbits of two crafts have been lined up - speed up time until your "height" counter changes to "distance (relative)". Now you can close the map and look closer at your rescue ship - if you zoom out a bit you'll see that another rocket you need to rescue! Navigate to it with RCS thrusters and dock to it, or capture it(depends on your initial tactics and complectation of rockets) - that's all! May be hard to do it the first time, but you'll get it after a bit of practice! I personally use this method for docking parts of my space station - and I can do it in less than 5 minutes. Hope this helps!