Filed extension and then filed return, now have two attempts to deduct payments

[lincolnandlucy]

First time filing and extension due to K1's not ready. I filed an extension, then TT dropped me on the landing page to file my return, which I assumed (wrongly) meant I was to also file the return. I thus filed the return as well. Unfortunately, now I know this was incorrect. However, both the extension was accepted as well as the filing. Now I have both attempts by the IRS to deduct the taxes owed for each, effectively paying taxes owed twice. I intentionally did not load my bank account to cover both, only one of the amounts...now I have a negative bank account balance and will see if there is an overdraft fee. That said, what are my options here? I can have the bank block the amount for the filing - not sure how the IRS views insufficient funds since the filing was accepted. If the IRS gets an insufficient funds response on the filing but not the extension, will the IRS figure this out on their own? Or am I stuck with having to transfer funds to the bank account, allow both charges to go through, then go back to the IRS and request a refund? TT didn't help because when I discovered I made an error to start with, the agent said the IRS would figure it out and not charge both...obviously, this was the not correct.

Updated: spoke with bank just now, learned that the payment while stated at Pending, was actually processed so no option to block payment (other than dispute which doesn't make sense). Now that both payments have processed, am I now limited to contacting the IRS and requesting refund? and if so, am I asking for refund of Extension amount or Filing amount, which oddly different by a few hundred dollars. I guess my indirect question is - which filing am I working from? the extension or the filing? "seems" like I am should be working from the filing being accepted, therefore I should be asking for the extension refunded, and then once I get my K1's, I should file an amendment? seems correct, but asking for feedback

[JohnB5677]

I suggest that you stop one of the payments so you do not have a negative balance.

• The IRS will figure out what you owe.
• Contact the IRS when after you stop payment and seek advice on what to do next.
• Just a note.  The IRS will not respond quickly.  Don't take it personal.

If you wish to contact the IRS, you can call toll-free at 800-829-1040 

[lincolnandlucy]

...thanks. but unfortunately, I cant stop the "payment" as its not a payment from my bank, rather an ACH withdrawal from checking, which has already processed despite showing "pending". which I understand means its just a ledger reconciliation across the banks. so...I had to transfer money from another account which should resolve the negative balance tonight.

So i'm accepting that I have made two payments to the IRS and I now need to get hold of the IRS and get one of them refunded. 

Biggest challenge is as you noted - I can't speak to anyone at the IRS. I'm stuck in the automated phone tree which doesn't know the answer to this unique predicament. And when I request to speak to a live agent, I am repeatedly told to call back during normal business hours...despite calling at 9:30am...

thx

[fanfare]

IRS computers will reconcile your payments and tax due. an overpayment will be returned to you -- eventually.

@lincolnandlucy 

[lincolnandlucy]

...eventually...