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Clark: You lied about having powers. How'd you get them?
Zod: From you. From your blood. When you saved me.
It's contradictory, isn't it? What is contradictory?

But then again, you are the greatest contradiction of all,
dedicating your life to the greater good and at the same time deceiving
those you love the most.
Clark: I'm the one who's been deceived.
Zod: Oh, come, come, (Come on?) Kal-El.
You have become far too calculating
to play the naive farm boy anymore.
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1.To me, the contradiction is Clark's ability (a side-effect really) to create a greater evil although his mission is exactly the opposite. By inadvertently giving more powers to his enemy, Clark made Zod an even stronger enemy, which obviously wasn't his intention.

2. Come, come, Kal-el (Come on?) I agree

The author used Kal-el (Clark's birth name) as a stylistic figure, which I think fits nice phonetically.
Comments  
MadhulkClark: You lied about having powers. How'd you get them?

It's contradictory, isn't it? What is contradictory?

Zod: Oh, come, come, (Come on?) Kal-El.

I'd would say that ironic also fits here. I think there is irony involved here, because Zod points out to Clark that he got his powers from him.

Perhaps come, come could mean something like don't be such a baby/don't act as if you never knew.
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 Ivanhr's reply was promoted to an answer.
Thanks, guys!