If you withdrew excess contributions from a 401k, that could only be done by the tax deadline for the following year (April 15, usually, although it depends on the year). If this was a pre-tax 401k, you have to report the withdrawn amounts as taxable income, because it was improperly subtracted from your taxable income on your W-2. If it was an after-tax (Roth) 401k, it should not have been taxable at all. Regardless of whether it was pre-tax or after-tax, you must also withdraw the earnings attributable to the excess contribution and report that as taxable income as well.
IRAs are similar. You generally need to withdraw the excess before the tax deadline. However, instead of reporting the excess withdrawal as taxable income, you would adjust your reported contributions. But you still need to withdraw, report, and pay tax on the earnings.
What assistance do you need at this point? Do you have an audit notice and need help responding? Or did you have the audit? If the audit is completed, and you have a final result, you can still appeal, but that is difficult and you really need your facts correct first.
It's hard to over-contribute to a 401k unless you change jobs during the year. Did you really over contribute to a 401k, or only to an IRA?
When did this occur? (Which tax year?)
What date was the withdrawal of excess contribution processed (when was it effective? May be a few days after you made the request.). Did you make the withdrawal before or after the due date of your tax return for that year?
Did you specifically request a withdrawal of excess contributions from the plan administrator? (It will usually be a separate form, not a regular withdrawal.)
How did you report the withdrawal on your tax return?