Keep in mind, that that's the intention.
In the original cannon, it was explained that MK as a tournament was tainted when Shang Tsung (and Goro) gained control of it. It stopped being a traditional tournament as he used Mortal Kombat as a chess board to move pieces around as he saw fit, in order to maintain control and get closer to win.
In this new cannon, seems that basis was maintained (as the story start already in the tournament), but they added that Shang Tsung made and agreement with the Lin Kuei with promises of power and other things after winning. Sub-Zero, Cyraz and Sektor were there as part of that agreement, to help into making earth-warriors lose the tournament and not participating directly on it. As seen with the Sub-Zero/Sonya fight. Then, when the Lin Kuei (Sub-zero and Cyrax) and Scorpion is second-guessing his loyalty to work with Quan Chi; with the Sub-Zero/Scorpion fight.