From what you have posted the lower amount is not correct unless on the W-2 you received the box is checked that you are a Statutory Employee. (This is not common).
Claiming you are a Statutory Employee means that you can take expenses against your W-2 income.
Since you checked the box when putting in the information for your return, you need to return to your W-2 and take the check out of Box 13 for the program to calculate your taxes correctly.
Link for more information about Statutory Employees
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