After you file

HELP!

When I filed my 2019 taxes, I owed $2,716. I filed and indicated to have the IRS take out my payment + the $20 penalty on 6/30/20. They did that correctly.

My problem is that I paid them in full prior to 6/30, through the IRS Direct payment site. ($1,318 on 4/21 and $1,398 on 5/26.) 

Thinking that the IRS would have noticed that I already paid my tax debt, they would not have taken out the auto debit on 6/30.

I was wrong and as a result, I have paid $2,716 too much.

How do I get that duplicate payment back?

I called [phone number removed] and they can not help me.  All they can do is direct me to [phone number removed], and I need to talk to a human to resolve this. The automated service can not help me.

What do I do?

Thank you