Tracing the folds:

• Fold 1 (diagonal): The paper is now a triangle. The folded corner = centre of original square.
• Fold 2 (triangle halved): The apex is still at the centre of the original square.

Punching at the folded corner (intersection of all folds = exact centre) means the punch goes through all 4 layers. But since the hole is at the centre, when unfolded it reveals 1 hole at the centre of the square — the layers were all stacked at that single point.

If the punch were at a non-fold point, you'd get 4 holes. But the apex/folded corner is a single geometric point — 1 hole appears.