If you are filing as Married Filling Separate you must both use the same deduction method.
You either have to use the standard deduction which would be $12,400 for each of you. or you must both use Itemized deductions.
If your wife has the mortgage deduction, and qualified for Itemized Deductions you will have to do the same, but will probably have a zero for deductions.
This may be why your returns were rejected.
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