GK one shot by clone in JMK tier III

Are you going for the veteran first? This is not usually too much of a problematic tier. So not sure what’s going wrong for you.

Here is a you tube achieving it without mods to showcase the kill order. Tier III is from 5.00 mins. 
https://www.youtube.com/watch?v=gl3_pyFCGX0

My guess is it was the Captain's 2nd special, which is basically Rex's stacking aerial damage special. I just tried Tier 3 three times, once by having the Veteran (basically Fives) sacrifice himself, the second and third time defeating Veteran first. The first time, the battle lasted long enough for the Captain (basically Rex) to kill of Obi. The second attempt didn't last long enough, the third one almost did, and only because I was deliberately prolonging it. You'd either have to have a lousy strategy or no mods to last long enough for the Captain to use his special.

He said he got vet first.

And I was clarifying because it’s the only thing that makes sense when it can be completed without mods before Rex’s execute. 

Gotcha

I did get Vet first. It's good to clarify. I've now done it a third time and did it the same way both successful attempts. I don't know what the heck happened at all. I think the 501st Captain got one, maybe two turns in before doing anything, but GK was just poofed out of existence. Totally unexpected.

And see, that's the thing, I did it the same way twice more afterwards and got it with no problems. I got Vet out first all three times. I don't know what the heck happened. Captain would've only gotten a turn or two in max before I took him out. This is a game issue, not a me issue.

To specify, I did the same thing all three attempts, and was successful the second and third, so I don't know what the heck happened to make GK just vanish like that without even a damage value.