Recurring Problem: Manga Designs

This could be a case of them cutting multiple covers at once.

I had the same problem with jeans. I order the exact same style and size, but they don't all fit the same. When I spoke to a Levi customer service person, they said they have multiple layers of fabric piled on top. Then the cutting blade presses down, and the fabric bends. As the top one is to short on measurements, the bottom most one is to long. So you want one in the middle.

I know paper isn't fabric, but it could be something similar. It's speed and efficiency over accuracy.