On the new Good Faith Estimates, the Upfront Mortgage Insurance Premium (UFMIP) can be rolled into the loan. And, in your case, most likely it is. However, the Dept. of HUD now requires the UFMIP be disclosed as a cost in a separate line item - even if it is rolled into the mortgage. So, it appears that you are paying it twice. In reality, you are not.
All costs, not matter who pays them and regardless of whether or not they are rolled into the mortgage, must be disclosed on the Good Faith Estimate as separate line items.