It's just to do with the speed, acceleration and deceleration, those kind of options. If it takes a longer time to slow down it'll shoot past it or can start slowing too early. I'm not entirely sure what the perfect settings are to stop immediately but maybe somebody knows.
If you want to move to an exact location you could try the rexrainbow moveto plugin, which doesn't have the need for physics and speed settings on an object. It simply moves the sprite to an exact location.