It's not clear whether you owe taxes with the W-2 omitted, or after you add it. Did you file an amended return to add the missing W-2? What is "it" that says you owe tax?
But in any case, you don't automatically get a refund for each W-2. Whether you owe or get a refund depends on your total tax for the year, for all jobs put together, and the total amount that you had withheld from your pay, for all jobs put together. If the total amount that you had withheld is more than your total tax, you get a refund of the excess that you paid. If the total amount that you had withheld is less than your total tax, you have to pay the difference.
Adding another W-2 changes the totals. It could go either way. It could change from a refund to a payment due, or from a payment due to a refund. If you got a refund on your original tax return, with one W-2 omitted, and then filed an amended return, the amended return takes into consideration the refund that you got on the original return. If the refund on the original return was more than you should have gotten, based on the correct totals for the year, then you have to pay some of it back.
Also note that increased income can affect tax credits ... review the new 1040 against the original 1040 to see what changed and how ... this is also reflected on the 1040X column B.
Look at the form 1040X …
Column A should have the figures from the original return, Column C the corrected figures and Column B the differences between the other 2 which needs an explanation on page 2 of the form 1040X.
If you completed it correctly you will see an entry on either line 16 OR 18:
On line 16 should be the amount you paid with your original return. If you paid nothing already then this line should be zero.
On line 18 should be the amount of your original refund you received. If you have not received your refund yet then you need to wait for it. If the refund changes from what you expected then this line must reflect that change.
Then you will see your extra refund on line 22 OR the new balance due you need to pay on line 20.
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