Elective deferral contributions need to be withheld from the payroll reported on a W2, not reported after. You can only deduct self-employment retirement contributions for non-w2 self-employment income. Also, if your wife owns the company and is issuing herself a W2, I'm assuming your wife's business is reporting as an S-Corp for tax purposes. You need to also enter the Schedule K-1 from her business' Form 1120S into your personal tax returns.
To get the contributions entered and receive the deductions, you will need to issue corrected W2s and a corrected business tax return for any employer or profit-sharing contributions made. Then enter the corrected W2s and Schedule K-1 to properly calculate your taxes.
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