LogFAQs > #924699657

And yeah, maybe its possible they graduate however many students and let the survival exercise trim that down to multiples of three.

BUT.

Kakashi passed all three of them without checking with anyone first, which seems unlikely to happen if they first needed to be sure of exact numbers. He was also willing to fail them all and expel them from the program, without first checking if an extra ninja or two were needed for another team.