The refund you are seeing is the result of your COMBINED incomes that were entered into your joint return. You are not getting "his and hers" refunds. When you added more income, your tax liability increased, so you saw your refund decrease. The program begins by giving you your personal exemption of $4050 plus your standard deduction—both of which lowered your taxable income. So you are not being taxed on as much of the income on that first W-2. Then you added taxable income--so the refund went down. Your refund (or tax due) is based on the total of your income, not “per W-2.” Wait until you have entered ALL of your income and deduction information. You can't really tell anything until it is all entered. That “refund monitor” does not mean anything until everything has been entered.
https://ttlc.intuit.com/questions/2273878-why-did-my-refund-drop-when-i-entered-another-w-2
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