Speed in super-cruise isn't linear, it's quadratic/exponential in relation to space-time compression. You're using a frame-shift drive which is, as its name implies, shifting the space-time frame of reference around you. It is compressing space-time.
In deep space where no gravity wells (a form of natural space-time compression) exist, and your FSD has had enough time to spool up fully, you are moving at full compression. Now when you're accelerating to move forwards, you're accelerating inside that compression bubble, which is also moving along with you (this is why ships look like very very long meteors, they're actually really stretched out energy bubbles).
The speed at which you're moving in 'normal' space-time is increased by orders of magnitude in relation to the hugely increased frame of reference (larger distances are being compressed into much smaller distances). In absolute terms, you're covering a much much greater distance at much greater speeds than you seem to be relative to yourself. This is what allows you to move at super-luminal speeds without actually moving faster than light (an impossibility).
As you near and enter a gravity well, your ships FSD (creating and controlling your local compression bubble) has an inverse relationship with the surrounding space-time compression of gravity wells. This is an automatic, inbuilt mechanism of the FSD for practical (and of course safety) reasons. Simply, the deeper you are into a gravity well, the closer your frame of reference will be to the 1:1 reference of the background space-time fabric. This will stop you from smashing through massive bodies at objectively super-luminal velocities and creating black holes, destroying the universe and such. Your destination lock also indicates to your ship computer that you need to be at a 1:1 compression when arriving at your destination, this applies the same behavior to your FSD as natural gravity wells, but in a much more controlled and drastic fashion (gravity wells will always slow you down, but unless you are specifically locked on to a given signal, under the right circumstances you are still able to achieve super-luminal speeds right through the deepest parts of a well, you will just be being slowed down drastically).
So, think of it like this. If you're in deep space, your FSD is fully spooled and you're traveling within your local bubble at full compression. You enter a gravity well and/or begin nearing your destination, as your drive reacts and your frame of reference shrinks, you will actually be speeding up relative to non compressed space as your absolute speed overtakes the rate at which your frame of reference is returning to 1:1. To counteract this, your ship begins decelerating at a rate proportional to the space-time rarefaction happening around you. you have some control over this, but it is largely automatic. You can for instance push the relationship into a relative velocity bias (faster than I should be) or a rarefaction bias (slower than I should be), or you can sit "in the blue" and allow the calculated deceleration to rarefaction ratio play out. This will always be the smoothest interpolation between frame states, but it is never the fastest.
To put it another way. If your rate of deceleration is faster than the rate of space-time rarefaction, you will be slowing down in absolute terms. If your rate of deceleration is the same as the rate of space-time rarefaction, you will be maintaining a constant velocity in absolute terms. If your rate of deceleration is slower than the rate of space-time rarefaction, you will be speeding up in absolute terms.
So "overshooting" is you having gone over the threshold of keeping your deceleration in relation to your absolute speed under the rate of decompression Vs distance to your destination. The confusion comes from the not directly observable relationship between your current frame size and your intended velocity at destination. This is why we seem to suddenly 'speed up' if we are, or are about to, over shoot. Objectively speaking, we are speeding up dramatically. More specifically: we are decelerating at a rate slower than our decompression.
There are two things at work, not just speed; but primarily a form of warping, with speed being applied within that (constantly shifting) frame of reference. Distance factors (current velocity/strength of spooled FSD) and size of massive body (strength/radius of gravity well) play a part in how this effects your ship. You can use this to your advantage when you get to know it well, 'riding' these elements to significantly cut down travel times, but until then, keep your throttle in the 'blue' and let the computer do the rest.
Hope this cleared things up.