Hope I can help
My car does the same thing once in a while. It has to do with the position sensor for the window since it has the express vent when opening the door. Don't know if its been fixed but try this:
Turn car on to accessory, close door, if windows up, roll down all the way without using the auto down, then roll all the way up again without auto up. This calibrates it. I've seen a message in the Driver Info Center telling me to do this. I don't know if you've seen the same. I hope this helps.