Incorrect 941 filed with IRS showing Balance Due!

I discovered the same issue on several of my client 941s around July 15th.  I contacted Intuit and was told I’d get a call back.  After a week I reached out through the Chat again with my case number. During a call with an experienced engineer, he suggested it was a result of a BETA change they had made recently surrounding the tax payments vs. tax transaction screens.  941 Line 13 is pulling from tax payments which of course for monthly filers were not submitted until the 15th.  Intuit system generated 941’s prior to that payment even though they have already deducted client funds for said tax payments.  Additionally, this engineer expressed the same concern that QBO was not going to fix their mistake and had not fully tested the application. It was my impression this error was under investigation for some time prior to my call but nothing was put out to the community. Instead a supervisor instructed him that they would wait for an IRS notice to handle for each client!  He says Payroll Core does not support Form 941x (Elite does) and so the agents have to manually process which he also said, they do not have enough support team to do that manually processing. I opted to handle the few monthly clients affected on my own to avoid any further issues but it’s a very frustrating scenario to explain to clients. The other side is the 941x does not have a line specific to correct line 13.  Research told me the IRS would “likely” fix it on their end but I could also put the details in the summary section which I did in the same 941x “original as filed” vs. “corrected line 13”. It was my intent to do as much to prevent that notice or at least have a paper trail for the client that explained it was a QBO error, which I did list in the summary of 941x as well. (hope this helps)

Since the semiweekly filers did not get caught up in this, I discussed with this engineer my plan to fool the system by changing all my monthly filers to semiweekly.  He agreed it would prevent the error if not corrected by QBO by Q3 2026.  I thought since QBO was already taking the funds and holding them until the 15th, I’d rather the IRS have it sooner to prevent the error on the automated filing side.  I too am very frustrated with the rising cost, and lack of accountability or communication when mistakes happen.  The engineer agreed there should have been a check in place to prevent this but it seems they tend to just push things out of BETA before all aspects are fully reviewed.  It just reminds me of all the software I’ve used and how many times it seems like it’s designed by engineers but not tested by accountants.  Good luck to you.