I must respectfully disagree. I have on many occasions reduced my speed to zero, the throttle indicator shows zero, and seen the actual speed of the ship increase! This has been in very close proximity to planets, which, if their gravity well is having any effect at all, should be causing me to decelerate! I just don't inderstand why this is happening.
The way I understand it is that your ship has a kind of "base" SC speed, which is the speed you would travel at if you were well away from gravitational attraction. Your acceleration/deceleration are defined in terms of this speed. You can kinda see what this means when you accelerate away when you're fuel scooping.
The actual speed you travel at is a function of your base speed and any gravitational modifiers. So, when you're moving at 300c and try to pass a nearby star, your actual speed reduces. When you've passed the star, your actual speed climbs to a faster speed (I think your SC speed tops out at 2001c) Now comes the tricky bit. If you attempt to approach a station from the planet side, but you end up moving
towards the station and thus
away from the planet, then your actual speed increases faster than your base speed is decreasing, so although you're slowing down in SC terms, the decreasing gravity is causing you to speed up more.
And... how do you fix it? Go to 75% throttle when you're miles out from bigger planets. Once you've switched to 75% throttle, so long as your base speed would get you to your destination in more than a "destination time" of 0:06, then you're safe and cannot overshoot. It's only if your throttle is >75% that you can overshoot.
Last bit, then it's time to go shopping: If you're around 5Mm away from the station and your speed is <1Mm/s, then hit 100% throttle. You'll accelerate, but you cannot go faster than 1Mm/s that close to your target. You need to be REALLY fast to hit "J" or "K" to exit SC as you'll be inside 1Mm doing around 750Mm/s. You get about 2/3 of a second to disengage!