I remember this all too well, your feelings are normal, but rest assured, what you are witnessing is totally normal! I realize every university is different, however, my DD ROTC scholarship did not show up until she passed her PFT. She was a 3 year, so we knew the tuition was on us and her academic scholarships, however, her university covers room and board for all scholarship recipients, even 3 year AD. It showed as a charge, until she passed the PFT then they covered it. Her ROTC did not inform Financial Aid of who was in ROTC until after they arrived, did their paperwork and passed the PFT, this coincided with school starting so she had already moved on campus prior to anything showing up in her financial aid package.
One thing I did that helped a lot was I got in touch with the financial aid officer, my DD gave me permission in her portal, and I talked through things with him. He handled all ROTC kiddos, Army and AF, so he was able to tell me "this is how it works" and then my normal anxieties were put to rest. This might be your first rodeo but it isn't theirs, so getting all the info will help put those fears to rest. I want to clarify, other than the financial aid counselor, my DD did all other communications, especially with her cadre and academically, that was the only place that had direct involvement in her 4 years in college. It sounds like you might already have talked to them, rest in what they told you. They can fix it retroactively, and it is pretty standard if it is ROTC related they will reverse any late fees that are incurred. We had the hurry up and wait every semester. Once she activated her scholarship she had to enter info into a portal to get payment, that had to get approved by the AROTC and then set for payment. Sometimes this didn't happen until more than a month after the semester started. Financial aid department never blinked, they expected it and it was always no problem. However by that time, FA knew she was ROTC and had the estimate in her portal, just pending. It was just that first semester that nothing showed up until after she showed up.