Sorry to bring up an old thread, if there's a newer thread let me know!
This just happened to my '16
cupra. Got a text from my neighbour at 6:30 telling me my windows are down. Of course it's been pissing it down all night, but not too heavily. You'd expect to see the interior soaked, but it was just the door cards and sides of the seats that were wet.
At first I thought I must have lent on the keys the day before, but all the doors were unlocked, and my keys hadn't been in my pocket since I got home from work in the afternoon. Now I think it must have happened near the time when my neighbour noticed it.
Actually this happened to a colleague of mine whose Leon FR estate's windows went down during a storm in the work car park. We both decided he must have lent on his keys in the office, but now I'm starting to think that it happened by itself too.
I will disable convenience window opening and see if that helps, but if it's some safety feature as mentioned above, then I'm probably out of luck!