USA Form 941 (and 941-X) issue

[Cody]

Situation: We are monthly Fed/FICA/Med filers. Our clerk accidentally added up all 3 months of our 3rd quarter withholding when she was paying the Sept withholding (online ACH payment). She realized she'd added up the entire quarter, went back into the online pay site and paid (another ACH payment) just the total for Sept (which is what should have happened the first time). End result: Our Fed/FICA/Med withholdings (deposits) for the 3rd qtr 2016 have been double paid.
However, on the 941 for that quarter she put the correct amounts actually withheld in all three month's deposit boxes on page 2. So the actual Form 941 is completely correct as far as wage totals and what we really withheld.

Question: How do we correct this? I've gone over the instructions for Form 941-X and it doesn't seem to address an error like this. It only refers to overreporting, but she didn't overreport on the 941, so there are no corrections to be done on it. She only overpaid the deposits section, but there isn't a place on 941-X for correcting that section.

Any idea how to file for a refund for the overpaid amount? Is there something I'm missing on Form 941-X that would address this?
Thanks for any help anyone can provide.

 

[Tyson]

Something similar happened to us when we switched payroll providers. A month's worth of taxes were overpaid. We got a letter from the IRS about six months later asking us how we would like to have our overpaid amounts refunded to us.

Perhaps you will get a letter too?

 

[Cody]

Thanks for the tip Tyson. I think that's what we'll do. Just do nothing and wait until they contact us.

 

[Houston Tax Attorney]

Don't wait too long. Overpayments that sit on the IRS's accounts can end up in the IRS's excess collections account. This just means that you cannot recoup the funds. The time period is usually the statute for filing a refund claim (later of 3 years from the date of the return or 2 years from the date of payment).

 

[Cody]

Thanks for replying Houston Atty. She actually did try to call the IRS but the hold time was over 1 1/2 hrs. With only one phone line and being a place of business, she couldn't keep the phone tied up on hold for hours so had to give up. I suspect the long wait is due to tax season, so once tax season is over we'll try calling again and see if we can find out how to initiate the refund process. Thanks again!