I think I see what the issue is or what you think is wrong in TurboTax.
But, we can't see your return and we don't know what you did.
The refund you didn't get goes on 1040-X anyway, as if you did get it.
See 1040-X line 18 overpayment if any , shown on original return.
Thus you must file as if you had already received your refund.
So TurboTax is correct.
Per 1040-X instructions:
"Any additional refund you are entitled to on Form 1040-X will
be sent separately from any refund you haven’t yet received
from your original return."
