A few thoughts:
You want the object to start slowing down when it’s a certain distance away. That distance is probably hit between the last frame and the current one. You could solve for that distance and between the frames and start applying the acceleration then. You could do something similar when the target is reached.
Another idea could be to adjust the acceleration to compensate since it will always start slowing down a bit late.
Simplest would be to clamp the position to stop at the target so it doesn’t overshoot.