The reason the program is saying you have excess contributions is because to be eligible to have an HSA, you must have a High Deductible Health Policy. Because the $325 had a code W in box 12 of your W-2, the amount was not included in your taxable income. You did not pay any income tax on the $325.
The excess contribution of $325 will be added back on your return as Other Income. That way you will be paying the income tax on the $325 that should have been in your taxable wages.
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