There is a valve that opens up to relieve fuel pressure in the fuel lines. On my Colorado (2005) there is a couple small "clunks" that it makes. The timing seems about like what you guys are talking about, 2-3 minutes after shutting the engine off.
My wifes previous car did this too, about the same time frame, but not the "double clunk" like my truck. I will have to pay attention to what the noise sounds like on her Cruze.
That's part of the fuel evaporative system, vent solenoid, now mostly located by the fuel tank exposed to salt and other nasty road stuff has to be opened to vent the tank into the carbon filled canister. It normally is only closed whenever the PCM decides to do a vacuum test on the system. Should be left opened with the key off. These valves to stick and maybe taking time to release. That can be dangerous if it stays closed, fuel evaporation can explode your tank.
As far as other weird stuff, BCM is always running as is the anti-thief system when the ignition key remote is in your pocket. BCM is waiting running a small routine for your remote to receive a command. Once it receives a valid command, it starts actions, one of them is beeping the horn if you have that enable. But these commands don't have to come from your remote, can be other sources of interference. One reason they tell you not to use your cell phones on airliners or hospitals.
Just one possibility, others are that huge maze of wires with any one of them giving an erratic connection. Or faults with the firmware stored in cheap flashram.
With of working with computers, we should all be familiar with glitches as they call them. MS solution was to reboot, and at first our cars were the same way. But PC's today are always hot waiting for a nano-ampere command to turn them on. Our new cars are the same way.
Never had that problem with a real hard contact switch, but those are expensive, now all nano-ampere commands. Even our TV is always hot, if the wife opens the blinds, IR rays from the sun can turn the TV on or off, solution here is simple, close the blinds.
You can go crazy trying to find the source of those glitches. Me for one, I am crazy, all caused by the microcontroller, flashram, and nano-ampere control signals.