If she received a scholarship AND cleared DoDMERB, then the fee "might" be covered by the scholarship depending on how the invoice is submitted to the unit. But if the university lists it as a separate fee, then the student (parent) typically pays that out of pocket.
The unit should notify the university of the scholarship, in which case they should not add in any late fees.
ALWAYS check with the unit for guidance. We have an expression within NROTC .... If you have seen one NROTC unit, you've seen jist one unit. Every one of us is unique based on state laws, university preferences, etc.