Seeing the damage, I wonder what the baptism of fire has taken long with the SAMD21.
It's the first time I see this type of damage done, although it can be done easily if assumptions are made that input/output/USB are not connected in any way or share a common ground in any way. I would be interested to find out what was actually smoked other than the SAMD21 and see how fixable it is.
I know this is a huge bummer for you on your first use. I hope you had a chance to at least visit the guide, maybe it was not completely clear that such a use case will really damage the CR.
I can offer to try to fix it for you for a small fee to cover parts if you're willing to also return it and pay for shipping.
Otherwise I can help assist in doing the repair yourself if you got the tools to do it and SMD doesn't scare you.
The USB charger did not have a 3 prong outlet so I made the assumption that its ground was floating but perhaps I was wrong in that assumption.
It doesn't matter what voltage you power your DUT from. CR only cares about the current passed through the input terminals, meaning - the voltage drop across the internal shunts, that's it. It can measure up to ~3.3A unidirectionally (DC) and ~1.65V bidirectionally (AC).
The USB has a GROUND, which I bet was the same GROUND as your 12V PSU. Even if it wasn't, if there's a potential difference between the input terminal + (12V) and the GROUND of the USB, that's really bad. That's more than enough to smoke the CR if you hook pass 12V through it from a different GROUND wired to input or output. Or if you form a closed circuit through the CR in any way shape or form (ie 12V at some point at input/output terminals) and the GROUND through the USB or at input/output or some of the headers.
You should never have USB connected unless everything else is floating so current cannot form a closed circuit through the CR. The only reason for USB is charging the battery, or perhaps data logging, if your DUT is on battery and the output is not connected (or connected to a floating DMM).
It's all explained in the guide, I should perhaps make some graphical drawings with big green OK connections and some with big red NO-NO connections. (anyone with ninja skills in that deparment?).