I'm never around when my car is done charging in the middle of the night, but my ASSUMPTION has always been that it stopped charging at the right percentage (e.g., 80%). Then some time after that, while the car is sleeping, measurements and re-calculation occurs and the display is updated to the newly calculated estimate (e.g., 83%). In other words, the charging is stopping at the point I set it to, but the car's estimate was off at the time and now it has been updated to something hopefully a bit more accurate (though I know it could be less accurate as well).
It's a minor annoyance that is really only noticeable because we have a digital display. If we had analog gauges, no one would notice that we're now half a needle-width closer to Full than we expected. It is annoying, however, to see my charge at 93% when it is clearly set for 90%, and given our guidance of not exceeding 90% on a regular basis it's even a little troubling.