I have a loan in which the APR was overstated due to a fee being included in the finance charge that shouldn't have been. This affected the APR enough so that the rate spread for HMDA is 3.02. Should we use the APR that was disclosed to the customer or what should have been the correct APR for the calculation?

For HMDA purposes you report the rate spread based on the APR disclosed at consummation. See page A-9 of the GIR.