Yes, it's possible. The IRS will always take your money. You are allowed to pay before you file your tax return. So you have now paid the tax that you owe, but you have not filed the tax return. You have to complete the filing. Either correct the reason for the rejection, if possible, and e-file it again, or print your tax return, sign it, and file it by mail.
You should have sent a Form 1040-V payment voucher with the check that you mailed. The IRS will match up the payment with your tax return when you file it.
