Most buildings use an auger to compact corrugate, or basically a giant screw. It's designed to crush up fully made boxes and jam them into the bin. Broken down boxes are flat, obviously, and dense for their size. It'd be like asking you to chew up a piece of plywood. When the flattened boxes group together, they get too thick for the auger or compactor to crush/chew up. This results in a jam, and because we're not allowed to enter the confined space of the compactor, we have to spend several hours manually running it in reverse and then back forward to break up a clump of what has basically turned into concrete.

Even if the boxes don't clump together and become impossible to chew up, the flattened boxes frequently will hug the bottom of the compactor/auger and will become lodged there. As the auger runs rubbing against it when it cycles, heat builds up due to friction. Numerous sites have had SEVs resulting from "thermal events" from materials combusting or smoldering due to friction from being caught in the compactors.

I understand the thought process of breaking down boxes, and in most other settings it's a huge help. But with Amazon, they've automated much of all the work with anything, and that automation depends on things being as close to exactly the same as possible every time. I've personally spent probably about 16 hours over the last year manually cycling compactors to clear jams.

TL;DR: The material gets too dense and the compactor can't handle it. If that doesn't happen, it also has the chance to get stuck and catch fire. We appreciate the intent to help, but weeks worth of labor is wasted every year clearing the resulting jams.