The IRS views taxes due as when you earn the money, not when you file the return. The system has annualized your wife's transfer and spread it out over the course of the year instead of setting it up as all-at-once along with your payment. So, the system is wrong but it's doing the best it can with the information it has.
Go to 'Other Tax Situations' in your federal return and click start next to underpayment penalties. The system will walk you through your income over the year and showing the math for where your transfer was made and where your payment was made should remove the penalty from your return.
@deuce7402
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