I efiled 2020 return, IRS accepted the return, funds withdrawn from bank, then I got a 4870 from IRS

I efiled my 2020 taxes before the due date of May 17, 2021.  State and IRS accepted the returns.  Since I owed the IRS, I inputted all the bank information for the withdrawal to take place.  Observing my bank account, the owed money was withdrawn! For the state, I recieved refund.  So I know I inputted the information via turbo tax correct.

 

The last week of May, apparently the IRS mailed me a Form 4870 that I receieved on the first week of June.  Initially thought this was a scam.  Then rechecked my bank account, and low and behold, the money was put back after a few weeks in the ether and was placed back in the first week of June.  The 4870 stated "RETURN: CHECK TRUNCATION ENTRY RETURN".  

 

How is this possible?  I never have been late with a payment over the last several years using turbo tax and have always used turbo tax to facilitate everything..  that is why I use Turbo Tax.  

 

Even after visiting the IRS website, I re-sent the payment and this time it was done via their website and not throught turbotax.  Then I get another notice that they missed tacking on interest charges.  Thank you IRS! [sarcasm]

 

I am not understanding how this happened and on top of that i am being penalized.