Hello there.
Something call my attention.
I did run four times colormunki display calibration process (twice "easy way" and twice "advanced") and I had four different results. I ran the process in the same room, with same ambient lights.
First and last, quite similar (small contrast difference), but call my attention the unsteadiness of results.

Is a Macbook Pro Retina Display. And calibration device is a X-Rite Colormunki Display.

I'd like to read your ideas.
See you.

Calibration (which in your case perhaps means profiling) and room light are not a guarantee for consistency. You still need hardware capable of maintaining its parameters stable. Only high class professional displays can do that. I don't know about your screen in particular but in laptop screens in general parameters vary all the time depending on battery level, temperature, variations in system load etc. Remember they are optimized mainly for low power consumption, not for color critical work.

Have you asked what Apple and X-Rite could say about that? It would be interesting to know.

I also do not know anything about the Macbook Pro Retina Display...
Usually this is a temperature difference...
That is why it is better to let the monitor/puck get stable temperature before doing the calibration.
If the monitor is too dark the puck will have difficult into reading the dark tones and this will lead to bigger differences.
If the monitor got poor electronics or aged, it can be less stable.
The lack of stability may not be perceived by the human eye, but by the measuring instrument.

I always test my colour calibration with a black to white gradient, horizontal, across the screen .. Shows up crushed blacks and banding like nothing else.

I've got an i1 Display 2 .. Couldn't get a good result with the software no matter what I tried – no better than doing it by eye with the Mac's software calibrator.

What worked for me was using a different bit of software – ColorEye Display Pro. Works with the i1 device and presumably others. A class above anything else I tried. Got some really awful results with other third party software.