Are you saying that you seeing the amount entered in box 5 of TurboTax's W-2 form affecting Taxable Income on Form 1040 line 10? If so, which of line above line 10 is changing? If it's line 6, what line of Schedule 1 is changing?
Items appearing on Schedule 4 are other taxes (including the additional Medicare tax), not income taxes. If you are married filing separately, your employer will not have withheld the entire amount of additional Medicare taxes necessary since an employer only withholds additional Medicare taxes on amounts in box 5 above $200,000 while an MFS filer is subject to additional Medicare taxes when box 5 is above $125,000. Or it's possible that the employer simply failed to withhold the proper amount of additional Medicare taxes since the increase in box 5 came from something other than wages. If Form 5989 line 18 is non-zero, you must pay additional Medicare taxes with your tax return.
