@mfbahler You might have to go back through the NY Allocation screen interview, particularly the "days worked in New York" method. Double-check to make sure that you have input the correct number of working days in New York versus days in the year and the number of "non-working days" so the program can figure out the correct amount of New York income. Also, you may want to check if filing New York as Married Filing Separately would be more advantageous, since your wife does not have New York income. In either case, deductions from her income are not based on New York sources, so you are correct in answering no on those questions.
With the pandemic from last year, there is no telling what differences you are seeing from your 2019 return versus your 2020 return, but that's the best way to compare why you are seeing a difference. Feel free to comment any additional clarifying information if you wish.
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