It sounds like your entries were correct. When scholarships exceed tuition and fees, then the balance of the scholarships becomes earned income. This earned income will increase the amount of tax owed and reduce your refund. 

One thing that TurboTax does is that it treats our MfA income as Self-Employment income, because that's how self-employment income is reported, and thus is subject to the ~15% FICA tax  However, this is wrong.    is what they are telling me