Is the refund that you received equal to the amount on Form 1040 line 20a of your tax return? If so, then the payment IS included. You don't necessarily get the whole payment back. It's combined with your withholding and any estimated tax payments that you made, and the total of all your payments (on line 18) is applied to your total tax (on line 15). Your refund is the net of line 18 minus line 15.
Presumably you made the payment with the extension because you thought you owed more tax than you had already paid. So it makes sense that you would not get the entire payment back.
If the refund that you received is less than the amount on line 20a, the IRS will send you a letter explaining why they reduced your refund. The letter might not come until a week or two after you got the refund. Don't do anything until you get the IRS letter. You'll decide what to do, if anything, after you see what the letter says.
