My wife has a 2008 Lincoln MKZ. On several occasions (including today) she has locked the car, closed the windows, etc. When returning to the car an hour later, she finds all the windows and the sunroof open. I didn’t believe her, but today I was with her.
It’s either a computer problem or a remote unlock problem. Check the remote first because it has a feature in it where…when you hold the “unlock” button down for 2 seconds the windows and moon roof will open. A button is sticking or a button is being held because of where the keys are stored and is being pressed by items in her purse or pocket. . . . OR, maybe she’s pressing unlock from farther away from the car and does’t realize the “windows open” feature has been engaged.
…I did this to myself once…While sitting in my livingroom watching tv, the panic horn goes off BEE BEE BEE BEE. I go to investigate…nuthin…turn it off and go sit down again BEE BEE BEE BEE !! Go to ivestigate and again no people, no dogs, nuthin. After much agrivation and investigation I finaly slapped myself in the forehead when I discovered that the wad of keys in my pocket was pushing on the remote buttons as I sat down !
…Moral of the story, check those two major causes of your issue happening naturaly by storing the keys in such a position or pushing too long on the unlock button not knowing the windows are cued to open.
One possible test could be to switch key/remotes with her letting her take and use the second remote to see if hers has sticking buttons. Also try taking the car yourself with her key/remote to see if the problem happens for you.
Does it always happen in the same parking location ? could someone else have remotes on the same frequency ? …Are you playing head games with her 
?
Thanks to both of you. The problem was her holding the “unlock” button down for more than 2 seconds.