Is Turbotax miscalculating NJ state income tax owed?

No, there are no known issues with TurboTax's calculations of New Jersey tax.  However, there's an aspect of New Jersey's "taxable income" that may be throwing you off. 

Line 39 of Form NJ-1040 is Taxable Income.  This amount represents your state taxable income before any property tax deduction on line 41 is applied.

Meanwhile, line 42 is your New Jersey Taxable Income (notice the different label).  This amount is your taxable income after the property tax deduction.  Your tax from the state tax table will be based on your line 42 amount, not your line 39 amount.  See the New Jersey Tax Table in the document linked above for more information. 

So, your tax table income is based on Form NJ-1040 line 42, not line 39, and this may be what's causing your confusion.  If not, feel free to post back.