I submitted payment with status as ‘filing jointly’ but then it would not allow me to finish filing. I then changed status and now asking for repayment?

You will need to contact the IRS for information. It might be easiest to set up an account with them.

IRS Individual Online Account  

• Taxpayers with a Social Security number or an Individual Taxpayer Identification Number can create or access their IRS Individual Online Account to get information they need to file their return.
• With an IRS Individual Online Account, people can:
• View balance owed, payment history and schedule payments.
• Cancel scheduled payments.
• Get transcripts.
• View or create payment plans.
• See digital copies of some IRS notices.
• View key data from their most recently filed tax return, including adjusted gross income.
• Validate bank accounts and save multiple accounts, eliminating the need to re-enter bank account information every time they make a payment.
• View, approve and electronically sign power of attorney and tax information authorizations from their tax professional.