The 'Fees that impact the APR missing for scenario' warning means that you haven't entered any fees that impact the APR. Remember that certain fees will be factored into the APR when calculating the APR.
Go to the 'Fees' screen and identify if any of the fees you've listed are APR Fees (finance charges) by editing the fee and checking the 'APR' checkbox.
Your company should be able to provide you with a list of fees that your company considers to be APR fees (prepaid finance charges).
You should have at least one fee entered on the 'Fees' screen for the respective scenario with a Fee Amount greater than $0 dollars with the APR checkbox checked and Lender Paid checkbox unchecked.
If you are using closing cost templates, remember to identify which fees are APR fees in your closing cost template.