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Is is possible to dispute IRS underpayment penalties?
When you say "set aside," you mean you saved to pay the tax due in April? That's underpaying. It's a rare exception the IRS makes for this penalty, hopefully it wasn't too large, and you now know how much to withhold through payroll deductions.  Problem is, this wasn't unusual, it was an oversight. You have no legitimate grounds to dispute. Sorry.