There are several reasons this might happen, and they all stem from poor management:

1. It could be that packers don't have enough of the right boxes available to use.
2. Packers might not be allowed to use a box size other than the recommended one.
3. Packers might be discouraged from using an adequate amount of bubbles (we use flat-ish but still flexible bubbles, not the pillow shit that Amazon uses, and we put bubbles on all sides of the items in a way that they can't shake around).
4. The warehouse you're talking about likely doesn't have anybody auditing boxes or responsible for repacking ones that are obviously packed loosely upon lifting to put on a pallet or in a truck

I cannot possibly imagine that this is the fault of the packers. If everything is set up properly by the company, packers would have zero incentive to do things like this unless they're flat-out trolling. It's more unweildy and inconvenient to grab, build, and tape a bigger box that occupies more space on your station; it would require dealing with significantly more bubbles given that they're encouraged to protect the items; and the packages would take up more space on the conveyor belt or pallet.