@lauren-palfi
I'm not sure exactly what you mean, so I've provided 2 scenarios below.
If you qualify to use "pay out of Federal refund", you won't see your refund amount go. You'll still get the same refund "on paper"; i.e., on your return. The fees are not taken by TurboTax until after the IRS approves and releases your refund.
Also, be aware that there is an extra $40 service fee for that option ($45 for California filers). You can avoid the additional fee by paying upfront with credit/debit card.
Or is it this? Is it telling you that you don't qualify to use the "pay out of refund" option? i.e., are you asking why you can't use it? If it's not allowing you to use that option, we can tell you some possible reasons why.