If a company has made an error it can correct its error by filing an amended form 941. Errors can be addressed. The IRS would the refund the overpayment to the company. There are no extra fees involved, and the IRS does not audit people because they correct a mistake they made. Correcting errors is done all the time. That comment was just made up in Disagreeable's head.Quoting Disagreeable
The company doesn't want to perform this work because it is a hassle. But if the company made the mistake, they should do it. It would be the right thing for them to do. But it is much easier not to take responsibility for an error and going to the trouble to make it right. So yes, as a practical matter, you will have to address it on your own tax return. Just make sure they've got your withholdings right going forward.

