It’s the same reason hotels over book. A certain percentage of people are expected to not show up. And sometimes that group lets down the side and actually shows up. It’s unfortunate, and they probably should have figured out some sort of “over flow” plan, but it happens, probably every single year at multiple schools without it hitting the news.
LOL, it’s not a hotel, it’s a graduation. Hotels overbook to ensure profits. Graduation ceremonies match the number of seats and the number of students and families that are going to show up - plus make room for mistakes, plus let people in to see their family members graduate anyway if there is a screw up. At least, that’s how it was back when human beings ran the schools.
Anyway, does it matter? It will be a cold day in hell before any school administrator is held responsible for the screwup, let alone punished. The same administrators who spent all year destroying minds with Common Core and forced hatred of heterosexuality and manliness, and dishing out draconian punishments under zero tolerance rules to their prison students.