I just posted this on another thread talking about the same issue...
I’ve had this problem (among others) since my Y was delivered. At first, I was told it was a bug with the app. That didn’t make any sense to me considering how random it was and how seemingly easy it would be to fix the app with an update. After a month of it occurring, I noticed that the rear windows were moving down slightly after being rolled all the way up. They aren’t opened and appear to be full closed but aren’t. It’s almost like a micro adjustment. But to be clear, they are moving slightly down after being fully closed. This obviously debunked the “it’s a bug in the app” excuse and I made a service appointment for them to look at a sensor that could be causing it.
When I arrived at my service appointment, my contact person told me he found a bulletin explaining the issue. According to him, when the ambient temperature drops below a certain temp the car will automatically slightly lower the window on any rear door that has been recently used to prevent it from freezing in the fully closed position. He made it sound like it was a more recent feature to help prevent windows from being shattered when frozen in place and hitting the frame of the car when people open and close them. This sounds plausible as I have heard of that happening to people and the rear window with the issue is usually the one on the drivers side. I use that door much more frequently to get stuff on and out of the car.
Next time you get the alert, go out to your car and open up the front door, what the rear window as you roll it up with the controls. See if it moves up slightly and back down. That’s what mine does. Hopefully, the service guy wasn’t making it up and it’s something they have programmed in to overcome the design issue of the frameless windows not clearing the body of the car when frozen in the fully closed position.