Has your DS asked the NCOIC to contact the Bursar's office? He may only need them to do that, and the Bursar will remove the amount.
The Bursar may require official paperwork from AROTC, and that is something you nor your DS can take care of.
The problem that we have come across with our 2 in college is that the Bursar will not allow us access into our kids accounts without their written permission. Trust me it is my pet peeve...you send me a bill to my home, but because they are 18 I can't talk to you about it.
Yet, there we stand trying to calm a child down because of an error created beyond their control, and scope of understanding how to rectify it.
My concern for you would be did they lock his account, and will not allow him to register for next semester. Our DS's school did that to him, and we didn't have 10K hanging out in our pockets. Worse yet, after we did get it resolved we had to fight the school because they slapped us with a $550 late fee, since ROTC didn't pay by the pre-determined date. Make sure that if the college charges late fees you have them removed. If you don't they can still find their accounts locked.
I have to say our DS's AFROTC career has been like Aglahad. Even this yr as a C400 (MSIV), they only rectified his stipend on the 15th of November. Prior to that they owed him 1250 bucks. They told him his checking account was bouncing it back. The same account they have deposited into for 3 yrs.
Finally, understand that the military has cut off dates for pay/stipend. I believe it is the 5th and the 24th of each month. If it is not rectified by the 5th, but on the 6th, he will not see it until the 1st of the month. If it is rectified on the 25th, it will be the 15th paycheck. I am not swearing by those dates, for all I know it could be the 9th and the 26th. I just do know that there are specific dates for pay/stipend.
Welcome to the military. This is just a taste of the AD world and how it can take 3 months to get your LES under control when you PCS, or switch banks.