I see additional ~4k of Medicate taxes, when looking at mine and my spouse W2, i think we have paid the 1.45 and the additional .09 medicare tax. How to correct it ?

The 0.9% Medicare already paid on your wages and reported on form W-2 has been reconciled on form 8959 and has been transferred as a credit on line 25c of form 1040.

So you are not paying the additional Medicare tax twice.