You need to be more specific in what size sheet but here is the deal and maybe you have the correct cutter in your Bindery to help with the problem:
The problem is the air trapped in the pile. Get rid of the air and your stacks will be much more acceptable. You have 2 options but it depends on your Cutter. #1 is if you have a jogger with a mash roller is to set it so it will roll over the stock multiple times. #2 is if you have a programmable cutter with an automatic mode there may be a option for clamp only. If so, step and repeat every few inches and this is what really takes it to the next level. If you really want it flat, you do this and make your first cut and then repeat with the pile in the other direction. Like I said, it depends on how you are set up and your workflow solutions in the Bindery. This does not slow me down any in my shop but I may be the exception. But I get great registration. I do this for 28X40 down to 12X18.
HTH,