I've experienced what you describe twice:
The first time I had boots that had too short and wide. My toes were touching, but there was so much room for the rest of my foot to move. That is probably some of the most pain I've experienced from any equipment.
The second was tightening my bindings too much. I really tighten my boots and bindings because I like that secure and in-control feeling. But I noticed I can overdo it sometimes. You don't even realize it, but I've started just pushing the heel strap tight without using the ratchet. Then giving it 1 or 2 clicks. That's all you really need.