2012 Mustang window problems

If it's the window drop down, those are known to have sporadic issues. Heck, my 2019 came with that same issue.
The contacts that report the doorlatch status are setup in the door in such a way that rainwater has a decent chance to get to those contacts. Worse still, the water runoff might not work so the water sits on those contacts and eventually evaporates.
As such the contacts might corrode, and thus provide a bad connection.

The moldule that controls the windows remains under the impression the door is NOT latched (and thus open), and will not move the window all the way up.

In my case took the door interior off, got the module out, cleaned the connectors, insulated it as much as possible to prevent water getting to it again, and reinstalled. Hasn't given me issues since.

Also see https://www.mustang6g.com/forums/threads/2018-window-randomly-moves-up-and-down-1-4-inch.143693/ - That one refers to https://www.mustangecoboost.net/threads/power-window-issue.20381/, specifically posty #12 for details (tho that one specifically refers to a pin in the connector not being seated properly).