I have had this problem, still do to be honest. Mini Cooper S (2004)
Had the car 1 year and its done it 3 times now !
Reading on here I was told to hold the electric window button in the up position for 30 seconds to reset some part of the system that controls the windows.
Did that and a few months later the windows did it again
It did it again 2 weeks ago but not done anything about it yet. I did read on hear to call the main dealer and get a software update, no idea how much thats gonna cost though !
I have tried pressing and holding unlock on the key but mine does not auto down the windows so it cant be that.