It sounds to me like the car was left on (and probably in neutral).

Reasoning:

The 12v battery was dead
The hybrid battery was run way down
The car was not out of gas

But:

In a Toyota the hybrid battery will charge in Park. (But NOT neutral). A Toyota would have run out of gas. I'm shocked this would have carried over to the Altima. Are you sure it wasn't charging in park - did you pull up the energy screen?

Is it possible that your wife also left the car in neutral when she parked it? (I'm assuming she regularly uses the parking brake)

I've shut off my car in drive a few times - it rolls!! - I don't use my parking brake)

Also:

In the Camry, the car beeps three times if you close the drivers door with the car left on. If you then push the lock button on the door it beeps a long beep. (and does not lock the door).

What I think happened:

The car was left on and in neutral. The parking brake was engaged so the car didn't roll when she left it.

The gas engine cannot start or charge the car in neutral. (this is why it didn't run out of gas as well)

At night the headlights come on and start discharging the hybrid battery. (The lights run off the hybrid battery via a 12v converter when the car is on.)

Eventually the hybrid battery ran low. At this point the car shuts itself off to protect the hybrid battery from running all the way down.

With car off, the lights then ran the 12v battery down.