You withdrew $10,100. Then you used $!00 of the money that you withdrew to make a state tax payment. It's the same as if you took the whole $10,100, then sent a check for $100 to the state. The amount that came out of your retirement account is $10,100.
Based on the question you posted a few days ago, it appears that you took an early distribution and used $10,000 towards the purchase of a first home. That $10,000 qualifies for an exception to the early distribution penalty. But $10,000 is the maximum for the first-home exception. Since you actually withdrew $10,100 you do have to pay the penalty on the additional $100.
