There are good and bad things about the wiring and control of modern cars...the old ones generally relied on actually switching the functions on and off by interrupting the voltage to them. Today, this is rarely the case. There's a computer that does it by taking an input signal from the switch which then talks to the module actually controlling the device we want to interact with. This means that generally, you can use microswitches that do not need heavy duty contacts and wires interconnecting them to the device. It also means that some things need to be listening so that they can react to the request and that switch itself needs power so it can generate the desired command. As a result, there are many modules that must listen to the computer bus when the car is shut down, get the command that the vehicle is now off, then shut themselves down.
An example of what I'm talking about is a CANbus activated trailer wiring interface module I recently installed. As an aftermarket item, it has some diagnostic LEDs on it so you can fathom out what's going on. It takes it about 10-15 seconds after you shut the vehicle off before it shuts itself down. Any one module that doesn't get the shutdown request, could, after time, discharge the battery. While an AGM battery lasts longer than a normal lead-acid car battery on deep discharge, no battery really likes to be deep cycled very much, and eventually, that will require replacement (hopefully, after you've discovered what isn't shutting down or is drawing more current than it should). Another example of a switch doing lots of things...think of the old headlight switch - a bunch of heavy wires and significant current going through it. The one on our GT has a 3 or 4 24g or so wires going into it. I've replaced mine with the one that provides the rear fog light functionality. So, there are the headlights, taillights, front/rear fogs all controlled by a little chip and the vehicle computer all through a few VERY small wires.
Any intermittent connection could allow one of the 'receivers' to miss the vehicle shutdown request. Just a little misrouting, chafing, dirty connection, could add enough noise to the data bus so that the digital message doesn't always get through. It's sort of a miracle that the things work as they do, but everything needs to be working as a system...finding the offending item can sometimes be tough if the computer doesn't see it. Today's car techs need a good computer/digital background to resolve this, and while the manufacturer's computer test device may be good, it can't find everything...the computer in the guys head is what makes the difference, and finding a good one can be tough!
So far (nearly two years), I like my vehicle...and will hopefully still like it for a fairly long time to come. I like to keep my cars for 6-8 years. Whether this one will fall into that trend or not is still yet to be seen.
Hope they can resolve your issue and restore your confidence in the vehicle's operation.