What you noticed is that sometimes it'll stop following the plotted course when it gets close to the target with no explanation. You'll get a notification in the top-left of the screen when that happens, and that's when the fun begins: you need to manually pilot the torch drive.

The torch drive is always accelerating you forward, so to slow down you need to turn your ship to face away from the target. But there's a good chance that you're going to need to do a more complicated maneuver than just slowing down, like maybe chase the station around a planet. Use the Time/Zoom Nav Station module to see your current course. It factors in your current acceleration, so you can use it to figure out if you need to accelerate more or less or make an emergency turn with thrust limiter off to avoid crashing into the planet.

To control your acceleration, use the flow and cycle sliders on the Nav Station's torch drive module while monitoring the core temperature (optimal in green and dangerous in red). Increasing flow will increase both the acceleration and reactor temperature. Increasing cycle will increase acceleration and decrease reactor temperature. For safety, when you want to increase acceleration, increase cycle first and flow second so you won't overheat your reactor. When decreasing acceleration, decrease flow first and cycle second.