Batons can break 2x4s. Hitting someone in the knee with one is a good way to cripple them for life, and that damage is far more than just a bruise. There will be ruptured bursas, torn ligaments, stretched or macerated tissue and tendons, and/or broken bones - any of which should have shown up clearly in the autopsy. If the ME says there was no evidence the guy was hit before being shot, then the officer was lying out his ass.
Batons *can* break 2x4's but I have also seen batons broken or bent on human bone.
The human body is at once weak and strong, depending on angles and force.