I want to be sure I understand. You said you were filling Married Filling Separate, but you are reporting it on the same form?
This would not be the correct procedure. If you file as Married Filling Jointly you post both of your incomes to the same form.
However, if you file Married Filing Separate you would each have your own form.
Your tax is being allocated to your wife because it thinks everything on it is for her tax return.
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