How does Turbotax calculate the Additional Medicare tax?

It seems turbotax calculates much higher tax due.

I have two W-2 forms (me and my spouse), by combining the total (box 6) we've already paid $11k.

Turbotax says we still owe $3500 tax, my understanding about the math of filing as married jointly case is: first $250000 is 1.45% rate, anything over that is 2.35%.

So let's say turbotax got our Total income as X, after deduction the total taxable income is Y,  so which is the actual math for Medicare Tax to be paid?

$250000 * 1.45% + (X - $250000) * 2.35%,  or 

$250000 * 1.45% + (Y - $250000) * 2.35%, or

$250000 * 1.45% + (Sum of Box 5 in all W-2, minus $250000, plus all other investment incomes after deduction) * 2.35% 

 

I am confused, because none of above maths result can match the amount from Turbotax, and both gave me much less tax due than turbotax, what did I miss ?