My DD attends a very small public IB high school (class size of 46) and they do not rank. USMA asked for a ranking percentile (top 10%, 20% etc) which the guidance counselor provided. In the case of her USAFA application, we reached out to AFA Admissions and they provided direction. The other suggestion would be to meet with the guidance counselor and have her open up the portal to see if he or she is making an error understanding or inputting the information. We have a very expereinced guidance counselor at my DD school, and her expereince with the SA application process is very limited. Good luck!
Regarding the comments related to the class rank, I agree with most of them. We have observed "gaming the system" at the 2 HS my DD has attended, taking easy courses to bump GPA. There is a price of admission, some choose to pay now, other defer to a later time which can in some cases have severe consequences.